# Usage of the metaseqR2 package

Panagiotis Moulos

#### 1 November 2022

# 1 RNA-Seq data analysis using mulitple statistical algorithms with metaseqR2

During the past years, a lot of packages have been developed for the analysis of RNA-Seq data, introducing several approaches. Many of them live in Bioconductor. Furthermore, different statistical approaches and heuristics are used in a continuous effort to improve overall accuracy. Such approaches include packages using the negative binomial distribution to model the null hypotheses (DESeq, DESeq2, edgeR, NBPSeq, “ABSSeq”), packages using Bayesian statistics (baySeq, EBSeq) or more hybrid solutions (NOISeq, voom). In addition, packages specialized to RNA-Seq data normalization have also been developed (EDASeq, RUVSeq). The first version of the metaseqR package (pronounced meta-seek-er) provided an interface to several algorithms for normalization and statistical analysis and at the same time provided PANDORA, a novel p-value combination method. PANDORA successfully combines several statistical algorithms by weighting their outcomes according to their performance with realistically simulated data sets generated from real data. Using simulated as well as real data, it was shown that PANDORA improves the overall detection of differentially expressed genes by reducing false hits while maintaining true positives. To our knowledge, PANDORA remains the only fully functional method proposing this combinatorial approach for the analysis of RNA-Seq data.

metaseqR2, is the continuation of metaseqR. While it has been (at times) heavily refactored, it still offers the same functionalities with as much backwards compatibility as possible. Like metaseqR, metaseqR2, incoporates several algorithms for normalization and statistical analysis. In particular, we extended the offered algorithms with DESeq2, ABSSeq and DSS. metaseqR2, like metaseqR also builds a full report with several interactive and non-interactive diagnostic plots so that the users can easily explore the results and have whatever they need for this part of their research in one place. The report has been modernized and remains one of its strongest points as it provides an automatically generated summary, based on the pipeline inputs and the results, which can be used directly as a draft in methods paragraph in scientific publications. It also provides a lot of diagnostic figures and each figure is accompanied by a small explanatory text, and a list of references according to the algorithms used in the pipeline. metaseqR2 continues to provide an interface for RNA-Seq data meta-analysis by providing the ability to use different algorithms for the statistical testing part and combining the p-values using popular published methods (e.g. Fisher’s method, Whitlock’s method), two package-specific methods (intersection, union of statistically significant results) and of course PANDORA.

Another major difference as compared to the older metaseqR package is the annotation system that is adopted by metaseqR2. More specifically, metaseqR2 introduces the `buildAnnotationDatabase` function which builds a local SQLite database with the supported by metaseqR annotations as well as additional versions added in the current package. This function, given a short and comprehensive number of arguments, automatically downloads, processes and imports to a portable database, all annotation types required by the main analysis pipeline. Therefore, the user neither has to embed nor download the required annotation each time. But most importantly, with the current package, the user is able also to provide an own GTF file with custom annotation elements that are the imported to the metaseqR2 database and annotation system and can be used for the respective analyses.

Apart from local database building, there also other major additions (such) as improved analysis for 3’UTR mRNA sequencing (Lexogen Quant-Seq protocol) which can be found towards the end of this page.

Throughout the rest of this document, `metaseqr2` refers to the name of the
analysis pipeline while metaseqR2 refers to the name of the package.

# 2 Getting started

## 2.1 Installation

To install the metaseqR2 package, start R and enter:

    if(!requireNamespace("BiocManager", quietly = TRUE))
        install.packages("BiocManager")
    BiocManager::install("metaseqR2")

## 2.2 Introduction

    library(metaseqR2)

Detailed instructions on how to run the metaseqr2 pipeline can be found under the main documentation of the metaseqR2 package.

Briefly, to run metaseqr2 you need:

1. Input RNA-Seq data. These can come in three forms:

- A text tab delimited file in a spreadsheet-like format containing at least unique gene identifiers (corresponding to one of metaseqR2 supported annotation sources, that is Ensembl, UCSC, RefSeq) or if you are using a custom annotation (with a GTF file), unique gene identifiers corresponding to this GTF file. This case is applicable in case of receiving a ready-made counts table from an external source, such as a sequencing facility or a public dataset.
- A text tab delimited file in a spreadsheet-like format containing all the required annotation elements and additional columns with read counts. This solution is applicable only for gene analysis (`transLevel = "gene"` and `countType = "gene"`). Generally, it is not recommended to embed the annotation and this case is supported only for backwards compatibility.
- A set of BAM files, aligned according to the mRNA sequencing protocol, usually a spliced aligner like HiSat or STAR. This is the recommended analysis procedure and the BAM files are declared in a targets text file.

2. A local annotation database. This is not required as all required annotation can be downloaded on the fly, but it is recommended for speed, if you have a lot of analyses to perform.
3. A list of statistical contrasts for which you wish to check differential expression
4. An internet connection so that the interactive report can be properly rendered, as the required JavaScript libraries are not embedded to the package. This is required only once as the report is then self-contained.

For demonstration purposes, a very small dataset (with embedded annotation) is included with the package.

## 2.3 Types of analyses performed with metaseqR2

Several types of differential analysis of gene expression can be performed and reported with metaseqR2 depending on the biological question asked and the type of data generated. For example, an investigator may be interested in gene- or transcript-level differential expression analysis when a 3’UTR sequencing kit has been used or interested for differential exon usage when a classical polyA RNA-Seq protocol has been applied.

These analysis types are being defined essentially by two arguments: * `countType` which can be `gene`, `exon`, `utr` corresponding to total RNA sequencing, polyA RNA sequencing or 3’ UTR sequencing respectively. * `transLevel` which can be `gene`, `transcript`, `exon` corresponding to differetial expression analysis using gene models (or essentially the dominant transcripts), individual transcripts or exons respectively.

Therefore, the selection of `countType="exon"` and `transLevel="gene"` assumes that we have a dataset where polyA RNA sequencing has been applied followed by splicing-aware alignment while `countType="utr"` and `transLevel="transcript"` assumes that we have a dataset where 3’UTR sequencing (e.g. Lexogen Quant-Seq) has been applied to look for differential expression based on read occupancy on the 3’ UTR regions.

The following combinations are available: * `countType="gene"`, `transLevel="gene"` for differential expression analysis using a pre-calculated counts table or BAM files from total RNA sequencing. * `countType="gene"`, `transLevel="transcript"` for differential expression analysis using a pre-calculated counts table or BAM files from total RNA sequencing and for each transcript. * `countType="gene"`, `transLevel="exon"` for differential expression analysis of exons using BAM files from polyA RNA sequencing. * `countType="exon"`, `transLevel="gene"` for differential expression analysis using BAM files from polyA RNA sequencing. * `countType="exon"`, `transLevel="transcript"` for differential expression analysis of transcripts using BAM files from total RNA sequencing. * `countType="utr"`, `transLevel="gene"` for differential expression analysis of genes using BAM files from 3’ UTR RNA sequencing. * `countType="utr"`, `transLevel="transcript"` for differential expression analysis of transcripts using BAM files from 3’ UTR RNA sequencing.

## 2.4 Data filtering

The metaseqR2 pipeline has several options for gene filtering at the gene and exon levels. These filters span various areas including: * The presence of a minimum number of reads in a fraction of the samples per condition or experiment-wise. * The exclusion of specific biotypes (e.g. exluding pseudogenes) * The filtering based on several expression attributes such as average read presence over n kbs or the exclusion of genes whose expression is below the expression of a set of genes known not to be expressed in the biological mechanism under investigation * Filters based on exon expression such as the minimum fraction of exons that should contain reads over a gene.

In addition, the metaseqR2 pipeline offers several analysis “presets” with respect to the filtering layers applied, the statistical analysis stringency and the amount of data exported.

All the aforementioned parameters are well-documented in the main manual of the package and the respective man pages.

# 3 Running the `metaseqr2` pipeline

Note: When conducting an analysis with metaseqR2, it is advised that you set a seed for random number generation using `set.seed()`. This should be set because some quality control charts in the metaseqR2 report are created by downsampling the initial dataset analyzed. Therefore, to guarantee the reproducibility of these plots, a seed must be provided.

    set.seed(42)

Running a metaseqr2 pipeline instance is quite straightforward. Again, see the examples in the main help page. Below, an example and the command window output follow:

    data("mm9GeneData",package="metaseqR2")

    head(mm9GeneCounts)

    ##                    chromosome   start     end            gene_id gc_content
    ## ENSMUSG00000090699      chr12 3023883 3025753 ENSMUSG00000090699     0.4441
    ## ENSMUSG00000092168      chr12 3082667 3087041 ENSMUSG00000092168     0.4649
    ## ENSMUSG00000079179      chr12 3236611 3249999 ENSMUSG00000079179     0.4178
    ## ENSMUSG00000020671      chr12 3247430 3309969 ENSMUSG00000020671     0.4023
    ## ENSMUSG00000069181      chr12 3343816 3357153 ENSMUSG00000069181     0.4508
    ## ENSMUSG00000020668      chr12 3365132 3406494 ENSMUSG00000020668     0.4756
    ##                    strand        biotype     gene_name e14.5_1 e14.5_2 a8w_1
    ## ENSMUSG00000090699      +     pseudogene        Gm9071       2       5    11
    ## ENSMUSG00000092168      +     pseudogene        Gm9075       0       0     1
    ## ENSMUSG00000079179      + protein_coding 1700012B15Rik     838     718   366
    ## ENSMUSG00000020671      - protein_coding         Rab10    1868    2004   977
    ## ENSMUSG00000069181      -        lincRNA       Gm17681      15      18    14
    ## ENSMUSG00000020668      + protein_coding         Kif3c     162     155   126
    ##                    a8w_2
    ## ENSMUSG00000090699    25
    ## ENSMUSG00000092168     0
    ## ENSMUSG00000079179   261
    ## ENSMUSG00000020671   807
    ## ENSMUSG00000069181    28
    ## ENSMUSG00000020668   122

    sampleListMm9

    ## $e14.5
    ## [1] "e14.5_1" "e14.5_2"
    ##
    ## $adult_8_weeks
    ## [1] "a8w_1" "a8w_2"

    libsizeListMm9

    ## $e14.5_1
    ## [1] 3102907
    ##
    ## $e14.5_2
    ## [1] 2067905
    ##
    ## $a8w_1
    ## [1] 3742059
    ##
    ## $a8w_2
    ## [1] 4403954

## 3.1 Analysis at the gene level with gene counts

Following, a full example with the informative messages that are printed in the command window:

    library(metaseqR2)

    data("mm9GeneData",package="metaseqR2")

    # You can explore the results in the session's temporary directory
    print(tempdir())

    ## [1] "F:\\biocbuild\\bbs-3.16-bioc\\tmpdir\\RtmpI9S1O3"

    result <- metaseqr2(
        counts=mm9GeneCounts,
        sampleList=sampleListMm9,
        contrast=c("adult_8_weeks_vs_e14.5"),
        libsizeList=libsizeListMm9,
        annotation="embedded",
        embedCols=list(
            idCol=4,
            gcCol=5,
            nameCol=8,
            btCol=7
        ),
        org="mm9",
        countType="gene",
        normalization="edger",
        statistics="edger",
        pcut=0.05,
        qcPlots=c(
            "mds","filtered","correl","pairwise","boxplot","gcbias",
            "lengthbias","meandiff","meanvar","deheatmap","volcano",
            "mastat"
        ),
        figFormat=c("png","pdf"),
        exportWhat=c("annotation","p_value","adj_p_value","fold_change"),
        exportScale=c("natural","log2"),
        exportValues="normalized",
        exportStats=c("mean","sd","cv"),
        exportWhere=file.path(tempdir(),"test1"),
        restrictCores=0.01,
        geneFilters=list(
             length=list(
                    length=500
             ),
             avgReads=list(
                    averagePerBp=100,
                    quantile=0.25
             ),
             expression=list(
                    median=TRUE,
                    mean=FALSE,
                    quantile=NA,
                    known=NA,
                    custom=NA
             ),
             biotype=getDefaults("biotypeFilter","mm9")
        ),
        outList=TRUE
    )

    ##
    ## 2022-11-01 21:22:18: Data processing started...

    ##
    ## Read counts file: imported custom data frame
    ## Conditions: e14.5, adult_8_weeks
    ## Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
    ## Samples to exclude: none
    ## Requested contrasts: adult_8_weeks_vs_e14.5
    ## Library sizes:
    ##   e14.5_1: 3102907
    ##   e14.5_2: 2067905
    ##   a8w_1: 3742059
    ##   a8w_2: 4403954
    ## Annotation: embedded
    ## Organism: mm9
    ## Reference source: ensembl
    ## Count type: gene
    ## Transcriptional level: gene
    ## Exon filters: minActiveExons
    ##   minActiveExons:
    ##     exonsPerGene: 5
    ##     minExons: 2
    ##     frac: 0.2
    ## Gene filters: length, avgReads, expression, biotype
    ##   length:
    ##     length: 500
    ##   avgReads:
    ##     averagePerBp: 100
    ##     quantile: 0.25
    ##   expression:
    ##     median: TRUE
    ##     mean: FALSE
    ##     quantile: NA
    ##     known: NA
    ##     custom: NA
    ##   biotype:
    ##     pseudogene: FALSE
    ##     snRNA: FALSE
    ##     protein_coding: FALSE
    ##     antisense: FALSE
    ##     miRNA: FALSE
    ##     lincRNA: FALSE
    ##     snoRNA: FALSE
    ##     processed_transcript: FALSE
    ##     misc_RNA: FALSE
    ##     rRNA: TRUE
    ##     sense_overlapping: FALSE
    ##     sense_intronic: FALSE
    ##     polymorphic_pseudogene: FALSE
    ##     non_coding: FALSE
    ##     three_prime_overlapping_ncrna: FALSE
    ##     IG_C_gene: FALSE
    ##     IG_J_gene: FALSE
    ##     IG_D_gene: FALSE
    ##     IG_V_gene: FALSE
    ##     ncrna_host: FALSE
    ## Filter application: postnorm
    ## Normalization algorithm: edger
    ## Normalization arguments:
    ##   method: TMM
    ##   logratioTrim: 0.3
    ##   sumTrim: 0.05
    ##   doWeighting: TRUE
    ##   Acutoff: -1e+10
    ##   p: 0.75
    ## Statistical algorithm(s): edger
    ## Statistical arguments:
    ##   edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
    ## Meta-analysis method: none
    ## Multiple testing correction: BH
    ## p-value threshold: 0.05
    ## Logarithmic transformation offset: 1
    ## Quality control plots: mds, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, deheatmap, volcano, mastat
    ## Figure format: png, pdf
    ## Output directory: F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpI9S1O3/test1
    ## Output data: annotation, p_value, adj_p_value, fold_change
    ## Output scale(s): natural, log2
    ## Output values: normalized
    ## Loading gene annotation...
    ## Saving gene model to F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpI9S1O3/test1/data/gene_model.RData
    ## Removing genes with zero counts in all samples...
    ## Normalizing with: edger
    ## Applying gene filter length...
    ##   Threshold below which ignored: 500
    ## Applying gene filter avgReads...
    ##   Threshold below which ignored: 0.0659629215631332
    ## Applying gene filter expression...
    ##   Threshold below which ignored: 68
    ## Applying gene filter biotype...
    ##   Biotypes ignored: rRNA
    ## 2106 genes filtered out
    ## 1681 genes remain after filtering
    ## Running statistical tests with: edger
    ##   Contrast: adult_8_weeks_vs_e14.5
    ##   Contrast adult_8_weeks_vs_e14.5: found 906 genes
    ## Building output files...
    ##   Contrast: adult_8_weeks_vs_e14.5
    ##     Adding non-filtered data...
    ##       binding annotation...
    ##       binding p-values...
    ##       binding FDRs...
    ##       binding natural normalized fold changes...
    ##       binding log2 normalized fold changes...
    ##     Writing output...
    ##     Adding filtered data...
    ##       binding annotation...
    ##       binding p-values...
    ##       binding FDRs...
    ##       binding natural normalized fold changes...
    ##       binding log2 normalized fold changes...
    ##     Writing output...
    ##     Adding report data...
    ##       binding annotation...
    ##       binding p-values...
    ##       binding FDRs...
    ##       binding log2 normalized fold changes...
    ##       binding normalized mean counts...
    ##       binding normalized mean counts...
    ## Creating quality control graphs...
    ## Plotting in png format...
    ##   Plotting mds...
    ##   Plotting correl...
    ##   Plotting pairwise...
    ##   Plotting boxplot...
    ##   Plotting gcbias...
    ##   Plotting lengthbias...
    ##   Plotting meandiff...
    ##   Plotting meanvar...
    ##   Plotting boxplot...
    ##   Plotting gcbias...
    ##   Plotting lengthbias...
    ##   Plotting meandiff...
    ##   Plotting meanvar...
    ##   Plotting deheatmap...
    ##   Contrast: adult_8_weeks_vs_e14.5
    ##   Plotting volcano...
    ##   Contrast: adult_8_weeks_vs_e14.5
    ##   Plotting mastat...
    ##   Contrast: adult_8_weeks_vs_e14.5
    ##   Plotting filtered...
    ## Plotting in pdf format...
    ##   Plotting mds...
    ##   Plotting correl...
    ##   Plotting pairwise...
    ##   Plotting boxplot...
    ##   Plotting gcbias...
    ##   Plotting lengthbias...
    ##   Plotting meandiff...
    ##   Plotting meanvar...
    ##   Plotting boxplot...
    ##   Plotting gcbias...
    ##   Plotting lengthbias...
    ##   Plotting meandiff...
    ##   Plotting meanvar...
    ##   Plotting deheatmap...
    ##   Contrast: adult_8_weeks_vs_e14.5
    ##   Plotting volcano...
    ##   Contrast: adult_8_weeks_vs_e14.5
    ##   Plotting mastat...
    ##   Contrast: adult_8_weeks_vs_e14.5
    ##   Plotting filtered...
    ##   Importing mds...
    ##   Importing pairwise...
    ##   Importing filtered...
    ##   Importing boxplot...
    ##   Importing gcbias...
    ##   Importing lengthbias...
    ##   Importing meandif...
    ##   Importing meanvar...
    ##   Importing volcano
    ##     adult_8_weeks_vs_e14.5 adult_8_weeks_vs_e14.5
    ##   Importing mastat
    ##     adult_8_weeks_vs_e14.5 adult_8_weeks_vs_e14.5
    ## Writing plot database in F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpI9S1O3/test1/data/reportdb.js
    ## Creating HTML report...
    ## Compressing figures...
    ## Downloading required JavaScript libraries...processing file: metaseqr2_report.Rmd
    ##
    ## Attaching package: 'gplots'
    ##
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    ## Loading required package: plotly
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    ## ======================
    ## Welcome to heatmaply version 1.4.0
    ##
    ## Type citation('heatmaply') for how to cite the package.
    ## Type ?heatmaply for the main documentation.
    ##
    ## The github page is: https://github.com/talgalili/heatmaply/
    ## Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
    ## You may ask questions at stackoverflow, use the r and heatmaply tags:
    ##   https://stackoverflow.com/questions/tagged/heatmaply
    ## ======================
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    ## output file: metaseqr2_report.knit.md

    ## "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc29906f193b7d.html --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "F:\biocbuild\bbs-3.16-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpI9S1O3\rmarkdown-str299058545f5f.html"

    ##
    ## Output created: F:/biocbuild/bbs-3.16-bioc/tmpdir/RtmpI9S1O3/test1/index.html
    ##
    ##
    ## 2022-11-01 21:22:57: Data processing finished!
    ##
    ##
    ## Total processing time: 39 seconds

To get a glimpse on the results, run:

    head(result[["data"]][["adult_8_weeks_vs_e14.5"]])

    ##                    chromosome     start       end            gene_id gc_content
    ## ENSMUSG00000000001       chr3 107910198 107949064 ENSMUSG00000000001      41.65
    ## ENSMUSG00000000339       chr3 116191881 116211126 ENSMUSG00000000339      43.09
    ## ENSMUSG00000000340       chr3 116215988 116252894 ENSMUSG00000000340      44.05
    ## ENSMUSG00000000420      chr18  24363845  24445319 ENSMUSG00000000420      40.82
    ## ENSMUSG00000000561       chr3 105762287 105787518 ENSMUSG00000000561      44.40
    ## ENSMUSG00000000562       chr3 105673776 105711846 ENSMUSG00000000562      45.35
    ##                    strand gene_name        biotype p-value_edger  FDR_edger
    ## ENSMUSG00000000001      -     Gnai3 protein_coding    0.09854676 0.16005517
    ## ENSMUSG00000000339      -     Rtcd1 protein_coding    0.20006583 0.28670985
    ## ENSMUSG00000000340      +       Dbt protein_coding    0.84076060 0.88674525
    ## ENSMUSG00000000420      +    Galnt1 protein_coding    0.01060295 0.02434911
    ## ENSMUSG00000000561      +     Wdr77 protein_coding    0.07624657 0.13145690
    ## ENSMUSG00000000562      +    Adora3 protein_coding    0.31863741 0.41944361
    ##                    natural_normalized_fold_change_adult_8_weeks_vs_e14.5
    ## ENSMUSG00000000001                                             0.5882636
    ## ENSMUSG00000000339                                             0.6194690
    ## ENSMUSG00000000340                                             1.0623330
    ## ENSMUSG00000000420                                             0.4348900
    ## ENSMUSG00000000561                                             0.5509965
    ## ENSMUSG00000000562                                             1.7258065
    ##                    log2_normalized_fold_change_adult_8_weeks_vs_e14.5
    ## ENSMUSG00000000001                                        -0.76546535
    ## ENSMUSG00000000339                                        -0.69089595
    ## ENSMUSG00000000340                                         0.08723612
    ## ENSMUSG00000000420                                        -1.20127760
    ## ENSMUSG00000000561                                        -0.85988498
    ## ENSMUSG00000000562                                         0.78727068

You may also want to check the interactive HTML report generated in the output directory defined by the `exportWhere` argument above.

Now, the same example but with more than one statistical selection algorithms, a different normalization, an analysis preset and filtering applied prior to normalization:

    library(metaseqR2)

    data("mm9GeneData",package="metaseqR2")

    result <- metaseqr2(
        counts=mm9GeneCounts,
        sampleList=sampleListMm9,
        contrast=c("adult_8_weeks_vs_e14.5"),
        libsizeList=libsizeListMm9,
        annotation="embedded",
        embedCols=list(
            idCol=4,
            gcCol=5,
            nameCol=8,
            btCol=7
        ),
        org="mm9",
        countType="gene",
        whenApplyFilter="prenorm",
        normalization="edaseq",
        statistics=c("deseq","edger"),
        metaP="fisher",
        #qcPlots=c(
        #    "mds","biodetection","countsbio","saturation","readnoise","filtered",
        #    "correl","pairwise","boxplot","gcbias","lengthbias","meandiff",
        #    "meanvar","rnacomp","deheatmap","volcano","mastat","biodist","statvenn"
        #),
        qcPlots=c(
            "mds","filtered","correl","pairwise","boxplot","gcbias",
            "lengthbias","meandiff","meanvar","deheatmap","volcano",
            "mastat"
        ),
        restrictCores=0.01,
        figFormat=c("png","pdf"),
        preset="medium_normal",
        exportWhere=file.path(tempdir(),"test2"),
        outList=TRUE
    )

    ## "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc29902c4879ce.html --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "F:\biocbuild\bbs-3.16-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpI9S1O3\rmarkdown-str299010857f8c.html"

A similar example with no filtering applied and no Venn diagram generation:

    library(metaseqR2)

    data("mm9GeneData",package="metaseqR2")

    result <- metaseqr2(
        counts=mm9GeneCounts,
        sampleList=sampleListMm9,
        contrast=c("adult_8_weeks_vs_e14.5"),
        libsizeList=libsizeListMm9,
        annotation="embedded",
        embedCols=list(
            idCol=4,
            gcCol=5,
            nameCol=8,
            btCol=7
        ),
        org="mm9",
        countType="gene",
        normalization="edaseq",
        statistics=c("deseq","edger"),
        metaP="fisher",
        qcPlots=c(
            "mds","filtered","correl","pairwise","boxplot","gcbias",
            "lengthbias","meandiff","meanvar","deheatmap","volcano",
            "mastat"
        ),
        restrictCores=0.01,
        figFormat=c("png","pdf"),
        preset="medium_normal",
        outList=TRUE,
        exportWhere=file.path(tempdir(),"test3")
    )

    ## "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc2990719e16f0.html --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "F:\biocbuild\bbs-3.16-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpI9S1O3\rmarkdown-str29903ab81c08.html"

Another example with the full PANDORA algorithm (not evaluated here):

    library(metaseqR2)

    data("mm9GeneData",package="metaseqR2")

    result <- metaseqr2(
        counts=mm9GeneCounts,
        sampleList=sampleListMm9,
        contrast=c("adult_8_weeks_vs_e14.5"),
        libsizeList=libsizeListMm9,
        annotation="embedded",
        embedCols=list(
            idCol=4,
            gcCol=5,
            nameCol=8,
            btCol=7
        ),
        org="mm9",
        countType="gene",
        normalization="edaseq",
        statistics=c("edger","limma"),
        metaP="fisher",
        figFormat="png",
        preset="medium_basic",
        qcPlots=c(
            "mds","filtered","correl","pairwise","boxplot","gcbias",
            "lengthbias","meandiff","meanvar","deheatmap","volcano",
            "mastat"
        ),
        restrictCores=0.01,
        outList=TRUE,
        exportWhere=file.path(tempdir(),"test4")
    )

    ## "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc299070c36299.html --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "F:\biocbuild\bbs-3.16-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "F:\biocbuild\bbs-3.16-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpI9S1O3\rmarkdown-str299010f033bc.html"

## 3.2 Analysis at the gene level with exon counts

Note: Be sure to have constructed a metaseqR2 annotation database prior to continuing with the following examples!

As example BAM files from a realistic dataset that can demonstrate the full availabilities of metaseqR2 do not fit within the Bioconductor package, you can find additional examples in our GitHub page where issues can be reported too.

## 3.3 Estimating p-value weights

In metaseqR2, the PANDORA algorithm is expaned with additional 3 algorithms. Briefly, PANDORA use of the area under False Discovery Curves to assess the performance of each statistical test with simulated datasets created from true datasets (e.g. your own dataset, as long as it has a sufficient number of replicates). Then, the performance assessment can be used to construct p-value weights for each test and use these weights to supply the p-value weights parameter of metaseqr2 when `metaP` is `"weight"`, `"pandora"` or `"whitlock"` (see the next sections for p-value combination methods). The following example shows how to create such weights (depending on the size of the dataset, it might take some time to run):

    data("mm9GeneData",package="metaseqR2")
    weights <- estimateAufcWeights(
        counts=as.matrix(mm9GeneCounts[,9:12]),
        normalization="edaseq",
        statistics=c("edger","limma"),
        nsim=1,N=10,ndeg=c(2,2),top=4,modelOrg="mm10",
        rc=0.01,libsizeGt=1e+5
    )

…and the weights…

    weights

    ## edger limma
    ##   0.5   0.5

## 3.4 Combining p-values from multiple tests

Although the main `metaseqr2` function takes care of p-value combination, sometimes there is the need of simply importing externally calculated p-values and using the respective metaseqR2 functions to produce combined p-values. We demonstrate this capability using p-values from all metaseqR2 supported algorithms, applied to data from Giakountis et al., 2016.

    data("hg19pvalues",package="metaseqR2")

    # Examine the data
    head(hg19pvalues)

    ##                     deseq      deseq2       edger     noiseq    bayseq
    ## ENSG00000004139 0.9376229 0.707127451 0.655534521 0.66858917 1.0000000
    ## ENSG00000004660 0.3059280 0.000032200 0.000020200 0.01750464 1.0000000
    ## ENSG00000004948 0.8752557 0.766905137 0.829416355 0.53040389 1.0000000
    ## ENSG00000007312 0.0277213 0.000384155 0.000000209 0.01558416 0.2147213
    ## ENSG00000007944 0.8995102 0.749182654 0.753981205 0.74932097 1.0000000
    ## ENSG00000008710 0.5847093 0.046782500 0.064277452 0.05570155 1.0000000
    ##                       limma       nbpseq      absseq          dss
    ## ENSG00000004139 0.634320805 0.7547977540 1.000000000 7.514558e-01
    ## ENSG00000004660 0.000727350 0.0011373140 0.221430162 1.747937e-03
    ## ENSG00000004948 0.736621379 0.7162818590 0.998049792 5.767438e-01
    ## ENSG00000007312 0.000219521 0.0000000487 0.000954742 1.570000e-09
    ## ENSG00000007944 0.784978571 0.7709520610 1.000000000 7.789785e-01
    ## ENSG00000008710 0.088718133 0.0644784670 0.989265394 1.191493e-01

    # Now combine the p-values using the Simes method
    pSimes <- apply(hg19pvalues,1,combineSimes)

    # The harmonic mean method with PANDORA weights
    w <- getWeights("human")
    pHarm <- apply(hg19pvalues,1,combineHarmonic,w)

    # The PANDORA method
    pPandora <- apply(hg19pvalues,1,combineWeight,w)

# 4 metaseqR2 components

## 4.1 Brief description

The metaseqR2 package includes several functions which are responsible for running each part of the pipeline (data reading and summarization, filtering, normalization, statistical analysis and meta-analysis and reporting). Although metaseqR2 is designed to run as a pipeline, where all the parameters for each individual part can be passed in the main function, several of the individual functions can be run separately so that the more experienced user can build custom pipelines. All the HTML help pages contain analytical documentation on how to run these functions, their inputs and outputs and contain basic examples. For example, runnning

    help(statEdger)

will open the help page of the wrapper function over the edgeR statistical testing algorithm which contains an example of data generation, processing, up to statistical selection.

Most of the diagnostic plots, work with simple matrices as inputs, so they can be easily used outside the main pipeline, as long as all the necessary arguments are given. In metaseqR2, most of the individual diagnostic plot creation functions are not exported, mostly for documentation simplicity and avoidance of confusion for non-experts. They can still be used by calling them as non-exported objects (e.g. `metaseqR2:::diagplotMds`). Finally, it should be noted that a report can be generated only when running the whole metaseqr2 pipeline and in the current version there is no support for generating custom reports. The final reports contains full interactive graphs and the required JavaScript libraries to generate them are automatically downloaded.

## 4.2 Backwards compatibility

If you have older pipelines based on metaseqR and the `metaseqr` function where the argument coding style is different (e.g. `sample.list` instead of `sampleList`) then `metaseqr2` will do its best to convert old arguments to new arguments so that old commands do not break and the only that should be changed is `metaseqr` to `metaseqr2`. Note however that you should not mix old and new arguments. In this case, the new pipeline will fail.

# 5 The report

In the end of each metaseqr2 pipeline run, a detailed HTML report of the procedure and the findings is produced. Apart from description of the process, all the input parameters and other data related to the differential expression analysis, the report contains a lot of interactive graphs. Specifically, all the quality control and result inspection plots are interactive. This is achieved by making extensive use of the JavaScript libraries Highcharts, Plotly and jvenn to create more user-friendly and directly explorable plots. By default metaseqr2 produces all available diagnostic plots, according always to input. For example, if the biotype feature is not available in a case where `annotation="embedded"`, plots like `biodetection` and `countsbio` will not be available. If not all diagnostic plots are not required, a selection can be made with the `qcPlots` argument, possibly making the report “lighter” and less browser-demanding.

The HTML report creation mechanism is through the packages rmarkdown and knitr. This means that the Pandoc libraries must be installed. A lot of details on this can be found in Pandoc’s website as well as knitr and rmarkdown websites and guides. Although the generic mechanism is more computationally demanding than standard HTML (e.g. using brew as in the previous metaseqR), the results are more standardized, cross-platform and fully reproducible.

During development, we found out that knitr faces certain difficulties in our settings, that is embedding a lot of predefined graphs in JSON format and all required libraries and data in a single HTML page. This situation led to crashes because of memory usage and of course, very large HTML files. We resolved this by using (according to usage scenario and where the report is intended to be seen):

1. A flavor of IndexedDB called Dexie
2. A JavaScript port of SQLite called sql.js

Regarding case (1), IndexedDB is a modern technology to create simple, in-browser object databases which has several usages, but mostly to avoid the burden of synchronously loading big-sized objects at the same time of simple HTML rendering. IndexedDB is supported by all modern browser and is essentially a replacement for `localStorage` which had space limitations. Dexie is a simple interface to IndexedDB. Thus, all the plot data are created and stored in Dexie for rendering when needed. This rendering method can be used both when the report is seen as a stand-alone document, locally, without the presence of a web server or internet connection, and is the default method.

Regarding case (2), all the predefined plot data are stored in a report-specific SQLite database which is then queried using sql.js. This way can be chosen when it is known that the report will be presented through a web server (e.g. Apache) as in any other case, modern web browser (except MS Edge) do not allow by default opening local files from an HTML page for security reasons. Also, sql.js is quite large as a library (altough downloaded once for recurring reports). This method produces slightly smaller files but is slightly slower. Using Dexie is the preferred and safest method for both scenarios.

In both cases, the serialized JSON used for Highcharts and jvenn plots is placed in `data/reportdb.js` when using Dexie or `data/reportdb.sqlite` when using sql.js. Experienced users can then open these files and tweak the plots as desired. The above paths are relative to the report’s location `exportWhere` arguments.

metaseqR2 report has the following sections, depending also on which diagnostic and exploration plots have been asked from the run command. As plots are categorized, if no plot from a specific category is asked, then this category will not appear. Below, the categories:

## 5.1 Summary

The Summary section is further categorized in several subsections. Specifically:

- Analysis summary: This section contains an auto-generated text that analytically describes the computational process followed and summarized the results of each step. This text can be used as is or with slight modifications in a Methods section of an article.
- Input options: This section provides a list of the input arguments to the pipeline in a more human-readable format.
- Filtering: This section reports in detail the number of filtered genes decomposed according to the number of genes removed by each applied filter.
- Differential expression: This section reports in detail the number of differentially expressed genes for each contrast, both when using only a p-value cutoff as well as an FDR cutoff (numbers in parentheses), that is, genes passing the multiple testing correction procedure selected. These numbers also are calculated based on a simple fold change cutoff in log2 scale. Finally, when multiple algorithms are used with p-value combination, this section reports all the findings analytically per algorithm.
- Command: This section contains the command used to run the metaseqr2 pipeline for users that want to experiment.
- Run log: This section contains critical messages displayed within the R session running `metaseqr2` displayed as a log.

## 5.2 Quality control

The Quality control section contains several interactive plots concerning the overall quality control of each sample provided as well as overall assessments. The quality control plots are the Multidimensional Scaling (MDS) plot, the Biotypes detection (Biodetection) plot, the Biotype abundance (Countsbio) plot, the Read saturation (Saturation) plot, the Read noise (ReadNoise) plot, the Correlation heatmap (Correlation), the Pairwise sample scatterplots (Pairwise) and the Filtered entities (Filtered) plot. Each plot is accompanied by a detailed description of what it depicts. Where multiple plot are available (e.g. one for each sample), a selection list on the top of the respective section allows the selection of the sample to be displayed.

## 5.3 Normalization

The Normalization section contains several interactive plots that can be used to inspect and assess the normalization procedure. Therefore, normalization plots are usually paired, showing the same data instance normalized and not normalized. The normalization plots are the Expression boxplots (Boxplots) plots, the GC content bias (GC bias) plots, the Gene length bias (Length bias) plots, the Within condition mean-difference (Mean-Difference) plots, the Mean-variance relationship (Mean-Variance) plot and the RNA composition (Rna composition) plot. Each plot is accompanied by a detailed description of what it depicts. Where multiple plot are available (e.g. one for each sample), a selection list on the top of the respective section allows the selection of the sample to be displayed.

## 5.4 Statistics

The Statistics section contains several interactive plots that can be used to inspect and explore the outcome of statistical testing procedures. The statistics plots are the Volcano plot (Volcano), the MA or Mean-Difference across conditions (MA) plot, the Expression heatmap (Heatmap) plot, the Chromosome and biotype distributions (Biodist) plot, the Venn diagram across statistical tests (StatVenn), the Venn diagram across contrasts (FoldVenn) and the Deregulogram. Each plot is accompanied by a detailed description of what it depicts. Please note that the heatmap plots show only the top percentage of differentially expressed genes as this is controlled by the `reportTop` parameter of the pipeline. When multiple plots are available (e.g. one for each contrast), a selection list on the top of the respective section allows the selection of the sample to be displayed.

## 5.5 Results

The Results section contains a snapshot of the differentially expressed genes in table format with basic information about each gene and some links to external resources. Certain columns of the table are colored according to significance. Larger bars and more intense colors indicate higher significance. For example, bar in the p_value column is larger if the genes has higher statistical significance and the fold change cell background is bright red if the gene is highly up-regulated. From the Results section, full gene lists can be downloaded in text tab-delimited format and viewed with a spreadsheet application like MS Excel. A selector on the top of the section above the table allows the display of different contrasts.

## 5.6 References

The References section contains bibliographical references regading the algorihtms used by the metaseqr2 pipeline and is adjusted according to the algorithms selected.

# 6 Genome browser tracks

metaseqR2 utilizes Bioconductor facilities to create normalized bigWig files. It also creates a link to open single stranded tracks in the genome browser and a track hub to display stranded tracks, in case where a stranded RNA-Seq protocol has been applied. Just make sure that their output directory is served by a web server like Apache. See main documentation for more details.

Please note that if requested, metaseqR2 will try to create tracks even with a custom organism. This is somewhat risky as

- the track generation may fail
- for heavily customized cases, you will manually have to crate aso .2bit files for visualization in e.g. the UCSC Genome Browser

Nevertheless, we have chosen to allow the track generation as, many times a user just uses slight modifications of e.g. the human genome annotation, where some elements may be manually curated, of elements are added (e.g. non-annotated non-coding RNAs). Therefore, in case of custom organisms, a warning is thrown but the functionality is not turned off. Please turn off manually if you are sure you do not want tracks. You may also use the `createSignalTracks` function directly.

# 7 List of required packages

Although this is not usually the content of a vignette, the complex nature of the package requires this list to be populated also here. Therefore, metaseqR2 would benefit from the existence of all the following packages:

- ABSSeq
- baySeq
- Biobase
- BiocGenerics
- BiocManager
- BiocParallel
- BiocStyle
- biomaRt
- Biostrings
- BSgenome
- corrplot
- DESeq
- DESeq2
- DSS
- DT
- EDASeq
- edgeR
- GenomeInfoDb
- GenomicAlignments
- GenomicFeatures
- GenomicRanges
- gplots
- graphics
- grDevices
- heatmaply
- htmltools
- httr
- IRanges
- jsonlite
- knitr
- limma
- log4r
- magrittr
- methods
- NBPSeq
- NOISeq
- pander
- parallel
- qvalue
- rmarkdown
- rmdformats
- RMySQL
- Rsamtools
- RSQLite
- rtracklayer
- RUnit
- S4Vectors
- stats
- stringr
- SummarizedExperiment
- survcomp
- TCC
- utils
- VennDiagram
- vsn
- zoo

A recent version of Pandoc is also required, ideally above 2.0.

# 8 Session Info

    sessionInfo()

    ## R version 4.2.1 (2022-06-23 ucrt)
    ## Platform: x86_64-w64-mingw32/x64 (64-bit)
    ## Running under: Windows Server x64 (build 20348)
    ##
    ## Matrix products: default
    ##
    ## locale:
    ## [1] LC_COLLATE=C
    ## [2] LC_CTYPE=English_United States.utf8
    ## [3] LC_MONETARY=English_United States.utf8
    ## [4] LC_NUMERIC=C
    ## [5] LC_TIME=English_United States.utf8
    ##
    ## attached base packages:
    ## [1] splines   stats4    stats     graphics  grDevices utils     datasets
    ## [8] methods   base
    ##
    ## other attached packages:
    ##  [1] pander_0.6.5                magrittr_2.0.3
    ##  [3] htmltools_0.5.3             heatmaply_1.4.0
    ##  [5] viridis_0.6.2               viridisLite_0.4.1
    ##  [7] plotly_4.10.0               ggplot2_3.3.6
    ##  [9] gplots_3.1.3                DT_0.26
    ## [11] rmdformats_1.0.4            knitr_1.40
    ## [13] metaseqR2_1.10.0            locfit_1.5-9.6
    ## [15] limma_3.54.0                DESeq2_1.38.0
    ## [17] SummarizedExperiment_1.28.0 Biobase_2.58.0
    ## [19] MatrixGenerics_1.10.0       matrixStats_0.62.0
    ## [21] GenomicRanges_1.50.0        GenomeInfoDb_1.34.0
    ## [23] IRanges_2.32.0              S4Vectors_0.36.0
    ## [25] BiocGenerics_0.44.0         BiocStyle_2.26.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] utf8_1.2.2               R.utils_2.12.1           tidyselect_1.2.0
    ##  [4] RSQLite_2.2.18           AnnotationDbi_1.60.0     htmlwidgets_1.5.4
    ##  [7] grid_4.2.1               TSP_1.2-1                BiocParallel_1.32.0
    ## [10] baySeq_2.32.0            munsell_0.5.0            preprocessCore_1.60.0
    ## [13] codetools_0.2-18         interp_1.1-3             future_1.28.0
    ## [16] withr_2.5.0              colorspace_2.0-3         filelock_1.0.2
    ## [19] ca_0.71.1                listenv_0.8.0            labeling_0.4.2
    ## [22] GenomeInfoDbData_1.2.9   hwriter_1.3.2.1          farver_2.1.1
    ## [25] bit64_4.0.5              rhdf5_2.42.0             parallelly_1.32.1
    ## [28] vctrs_0.5.0              generics_0.1.3           lambda.r_1.2.4
    ## [31] xfun_0.34                BiocFileCache_2.6.0      EDASeq_2.32.0
    ## [34] R6_2.5.1                 seriation_1.4.0          NBPSeq_0.3.1
    ## [37] bitops_1.0-7             rhdf5filters_1.10.0      cachem_1.0.6
    ## [40] DelayedArray_0.24.0      assertthat_0.2.1         BiocIO_1.8.0
    ## [43] scales_1.2.1             bsseq_1.34.0             gtable_0.3.1
    ## [46] affy_1.76.0              globals_0.16.1           log4r_0.4.2
    ## [49] rlang_1.0.6              genefilter_1.80.0        rtracklayer_1.58.0
    ## [52] lazyeval_0.2.2           DSS_2.46.0               BiocManager_1.30.19
    ## [55] yaml_2.3.6               reshape2_1.4.4           abind_1.4-5
    ## [58] crosstalk_1.2.0          GenomicFeatures_1.50.0   qvalue_2.30.0
    ## [61] lava_1.7.0               tools_4.2.1              bookdown_0.29
    ## [64] affyio_1.68.0            ellipsis_0.3.2           jquerylib_0.1.4
    ## [67] RColorBrewer_1.1-3       Rcpp_1.0.9               plyr_1.8.7
    ## [70] sparseMatrixStats_1.10.0 progress_1.2.2           zlibbioc_1.44.0
    ## [73] purrr_0.3.5              RCurl_1.98-1.9           prettyunits_1.1.1
    ##  [ reached getOption("max.print") -- omitted 88 entries ]