# Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer

## Documentation for package ‘omicsViewer’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

app_module | Application level 0 module
app_ui | Application level 0 UI
asEsetWithAttr | Convert SummarizedExperiment to ExpressionSet retaining all attributes
correlationAnalysis | Correlating a expression matrix with phenotypical variables
csc2list | convert a column compressed sparse matrix to a list
downloadUPRefProteome | get uniprot reference proteome IDs
draw_roc_pr | Drawing ROC and PR curve
exprspca | Perform PCA and prepare results for 'omicsViewer'
extendMetaData | Add extra columns to the phenoData/colData or featureData/rowData in ExpressionSet/SummarizedExperiment
extendMetaData-method | Add extra columns to the phenoData/colData or featureData/rowData in ExpressionSet/SummarizedExperiment
fgsea1 | Wrapper of fgseaMultilevel function to take binary gene set matrix as input
fillNA | Filling NAs in a matrix using constants calculated from user the defined function
filterRow | Filter out rows of expression matrix
getAutoRIF | Get genes associated with search terms and AutoRIF annotations
getMQParams | Parse mqpar.xml file
getUPRefProteomeID | get uniprot reference proteome IDs
gsAnnotIdList | Annotation of gene/protein function using multiple IDs.
hasAttr | Check whether an object has an attribute
hclust2str | Convert hclust object to/from single character
list2csc | convert a list to column compressed sparse matrix
multi.t.test | Function to perform multiple t-tests on an expression matrix
nColors | Generating k distinct colors
normalize.nQuantiles | Normalization using n quantiles
normalize.totsum | Normalize total sum
normalizeColWise | Column-wise normalization of expression matrix
normalizeData | Normalized expression matrix
omicsViewer | Start omicsViewer
parseDatTerm | Extract function annotation from uniprot .dat file
plotly_boxplot_module | Shiny module for boxplot using plotly - Module
plotly_boxplot_ui | Shiny module for boxplot using plotly - UI
plotly_scatter_module | Shiny module for scatter plot using plotly - Module
plotly_scatter_ui | Shiny module for scatter plot using plotly - UI
plot_roc_pr_module | Shiny module for boxplot using plotly - Module
prepOmicsViewer | Prepare object to be viewed by omicsViewer
read.proteinGroups | Reading proteinGroup table of MaxQuant output
read.proteinGroups.lf | Read protein groups output of maxquant output and split it to columns
readESVObj | Read the object of SummarizedExperiment or ExpressetSet to be visualized using omicsViewer
read_gmt | Reading gene set .gmt file
removeVarQC | Removing variance of reference samples
rowshift | Row-wise normalization of expression matrix with or without reference sample
saveOmicsViewerDb | Save the xcmsViewer result object as sqlite database
saveOmicsViewerDb-method | Save the xcmsViewer result object as sqlite database
str2hclust | Convert hclust object to/from single character
triselector_module | The three-step selector - the module function
triselector_ui | The three-step selector - the ui function
trisetter | Create a nx3 matrix that can be use for triselector given a meta and expression table
validMQFolder | MQ folder validator Validate whether a folder is a MQ output folder
varSelector | variable selector