# systemPipeR: NGS workflow and report generation environment

## Documentation for package ‘systemPipeR’ version 2.7.0

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

## Help Pages

A B C D E F G I L M N O P R S T U V W Y misc

systemPipeR-package | systemPipeR package for Workflow Environment

## -- A --

addAssay | Extension accessor methods for SummarizedExperiment object
addAssay-method | Extension accessor methods for SummarizedExperiment object
addAssay-methods | Extension accessor methods for SummarizedExperiment object
addMetadata | Extension accessor methods for SummarizedExperiment object
addMetadata-method | Extension accessor methods for SummarizedExperiment object
addMetadata-methods | Extension accessor methods for SummarizedExperiment object
addResources | Class '"SYSargsList"'
addResources-method | Class '"SYSargsList"'
alignStats | Alignment statistics
appendCodeLine-method | Class '"LineWise"'
appendCodeLine<- | Class '"SYSargsList"'
appendCodeLine<--method | Class '"LineWise"'
appendCodeLine<--method | Class '"SYSargsList"'
appendParam | Accessories function to modify the Command-line Version 1
appendParam2 | Accessories function to modify the Command-line Version 2
appendStep<- | Class '"SYSargsList"'
appendStep<--method | Class '"SYSargsList"'
as.list-method | Class '"INTERSECTset"'
as.list-method | Class '"VENNset"'
available_modules-method | Class '"EnvModules"'

## -- B --

baseCommand | Class '"SYSargsList"'
baseCommand-method | Class '"SYSargs2"'
baseCommand-method | Class '"SYSargsList"'

## -- C --

catDB-class | Class '"catDB"'
catlist | catDB accessor methods
catlist-method | Class '"catDB"'
catlist-methods | catDB accessor methods
catmap | catDB accessor methods
catmap-method | Class '"catDB"'
catmap-methods | catDB accessor methods
check.outfiles | Checking if the outfiles files exist
check.output | Checking if the outfiles files exist
clt | Class '"SYSargs2"'
clt-method | Class '"SYSargs2"'
clusterRun | Submit command-line tools to cluster
cmdlist | Class '"SYSargsList"'
cmdlist-method | Class '"SYSargs2"'
cmdlist-method | Class '"SYSargsList"'
cmdToCwl | Class '"SYSargs2"'
cmdToCwl-method | Class '"SYSargs2"'
cmdToCwl<- | Class '"SYSargs2"'
cmdToCwl<--method | Class '"SYSargs2"'
codeChunkStart | Class '"LineWise"'
codeChunkStart-method | Class '"LineWise"'
codeLine | Class '"SYSargsList"'
codeLine-method | Class '"LineWise"'
codeLine-method | Class '"SYSargsList"'
coerce-method | Class '"EnvModules"'
coerce-method | Class '"INTERSECTset"'
coerce-method | Class '"LineWise"'
coerce-method | Class '"SYSargs"'
coerce-method | Class '"SYSargs2"'
coerce-method | Class '"SYSargsList"'
coerce-method | Class '"VENNset"'
coerce-method | Class '"catDB"'
combineVarReports | Generate Variant Report
complexitylevels | Set Intersect and Venn Diagram Functions
complexitylevels-method | Class '"INTERSECTset"'
complexitylevels-method | Class '"VENNset"'
complexitylevels-methods | Set Intersect and Venn Diagram Functions
config.param | Adding param file
configWF | Workflow Steps Selection
copyEnvir | Class '"SYSargsList"'
copyEnvir-method | Class '"SYSargsList"'
cores | SYSargs accessor methods
cores-method | Class '"SYSargs"'
cores-methods | SYSargs accessor methods
countRangeset | Read counting for several range sets
createParam | createParam
createParamFiles | createParam
cwlFilesUpdate | Update CWL description files

## -- D --

default_modules-method | Class '"EnvModules"'
dependency | Class '"SYSargsList"'
dependency-method | Class '"LineWise"'
dependency-method | Class '"SYSargsList"'
dependency<- | Class '"SYSargsList"'
dependency<--method | Class '"SYSargsList"'

## -- E --

EnvModules-class | Class '"EnvModules"'
EnvModules-method | Class '"EnvModules"'
evalCode | Toggles option 'eval' on the RMarkdown files

## -- F --

featureCoverage | Genome read coverage by transcript models
featuretypeCounts | Plot read distribution across genomic features
files | Class '"SYSargs2"'
files-method | Class '"LineWise"'
files-method | Class '"SYSargs2"'
filterDEGs | Filter and plot DEG results
filterVars | Filter VCF files

## -- G --

genFeatures | Generate feature ranges from TxDb
getColumn | Class '"SYSargsList"'
getColumn-method | Class '"SYSargsList"'
goBarplot | GO term enrichment analysis for large numbers of gene sets
GOCluster_Report | GO term enrichment analysis for large numbers of gene sets
GOHyperGAll | GO term enrichment analysis for large numbers of gene sets
GOHyperGAll_Simplify | GO term enrichment analysis for large numbers of gene sets
GOHyperGAll_Subset | GO term enrichment analysis for large numbers of gene sets

## -- I --

idconv | catDB accessor methods
idconv-method | Class '"catDB"'
idconv-methods | catDB accessor methods
importWF | Import R Markdown file as workflow
infile1 | SYSargs accessor methods
infile1-method | Class '"SYSargs"'
infile1-method | Class '"SYSargs2"'
infile1-methods | SYSargs accessor methods
infile2 | SYSargs accessor methods
infile2-method | Class '"SYSargs"'
infile2-method | Class '"SYSargs2"'
infile2-methods | SYSargs accessor methods
input | Class '"SYSargs2"'
input-method | Class '"SYSargs2"'
inputvars | Class '"SYSargs2"'
inputvars-method | Class '"SYSargs2"'
internal_outfiles | Class '"SYSargs2"'
internal_outfiles-method | Class '"SYSargs2"'
intersectlist | Set Intersect and Venn Diagram Functions
intersectlist-method | Class '"INTERSECTset"'
intersectlist-methods | Set Intersect and Venn Diagram Functions
intersectmatrix | Set Intersect and Venn Diagram Functions
intersectmatrix-method | Class '"INTERSECTset"'
intersectmatrix-method | Class '"VENNset"'
intersectmatrix-methods | Set Intersect and Venn Diagram Functions
INTERSECTset-class | Class '"INTERSECTset"'

## -- L --

length-method | Class '"INTERSECTset"'
length-method | Class '"LineWise"'
length-method | Class '"SYSargs"'
length-method | Class '"SYSargs2"'
length-method | Class '"SYSargsList"'
length-method | Class '"VENNset"'
LineWise | Class '"LineWise"'
linewise | Class '"LineWise"'
LineWise-class | Class '"LineWise"'
linewise-method | Class '"LineWise"'
loaded_modules-method | Class '"EnvModules"'
loadWF | Constructs SYSargs2 object from CWL param and targets files
loadWorkflow | Constructs SYSargs2 object from CWL param and targets files

## -- M --

makeCATdb | GO term enrichment analysis for large numbers of gene sets
mergeBamByFactor | Merge BAM files based on factor
module | Interface to allow full use of the Environment Modules system for Unix
moduleAvail | Interface to allow full use of the Environment Modules system for Unix
moduleClear | Interface to allow full use of the Environment Modules system for Unix
modulecmd-method | Class '"EnvModules"'
moduleInit | Interface to allow full use of the Environment Modules system for Unix
modulelist | Interface to allow full use of the Environment Modules system for Unix
moduleload | Interface to allow full use of the Environment Modules system for Unix
modules | Class '"SYSargs2"'
modules-method | Class '"SYSargs"'
modules-method | Class '"SYSargs2"'
modules-methods | SYSargs accessor methods
moduleUnload | Interface to allow full use of the Environment Modules system for Unix

## -- N --

names-method | Class '"EnvModules"'
names-method | Class '"INTERSECTset"'
names-method | Class '"LineWise"'
names-method | Class '"SYSargs"'
names-method | Class '"SYSargs2"'
names-method | Class '"SYSargsList"'
names-method | Class '"VENNset"'
names-method | Class '"catDB"'

## -- O --

olBarplot | Bar plot for intersect sets
olRanges | Identify Range Overlaps for IRanges and GRanges Object
other | SYSargs accessor methods
other-method | Class '"SYSargs"'
other-methods | SYSargs accessor methods
outfile1 | SYSargs accessor methods
outfile1-method | Class '"SYSargs"'
outfile1-methods | SYSargs accessor methods
outfiles | Class '"SYSargsList"'
outfiles-method | Class '"SYSargsList"'
outpaths | SYSargs accessor methods
outpaths-method | Class '"SYSargs"'
outpaths-methods | SYSargs accessor methods
output | Class '"SYSargs2"'
output-method | Class '"SYSargs2"'
output_update | Updates the output files paths in the 'SYSargs2' object
overLapper | Set Intersect and Venn Diagram Functions

## -- P --

plotfeatureCoverage | Plot feature coverage results
plotfeaturetypeCounts | Plot read distribution across genomic features
plotWF | Visualize SPR workflow and status
plotwfOutput | Visualize SPR workflow and status
predORF | Predict ORFs
preprocessReads | Run custom read preprocessing functions
printParam | Accessories function to modify the Command-line Version 1
printParam2 | Accessories function to modify the Command-line Version 2
projectInfo | Class '"SYSargsList"'
projectInfo-method | Class '"SYSargsList"'

## -- R --

readComp | Import sample comparisons from targets file
reference | SYSargs accessor methods
reference-method | Class '"SYSargs"'
reference-methods | SYSargs accessor methods
removeParam2 | Accessories function to modify the Command-line Version 2
renameParam | Accessories function to modify the Command-line Version 1
renameParam2 | Accessories function to modify the Command-line Version 2
renameStep<- | Class '"SYSargsList"'
renameStep<--method | Class '"SYSargsList"'
renderLogs | Render RMarkdown Logs Report
renderPlotwf | Visualize SPR workflow and status
renderReport | Render RMarkdown Report
renderWF | Constructs SYSargs2 object from CWL param and targets files
replaceCodeLine-method | Class '"LineWise"'
replaceCodeLine<- | Class '"SYSargsList"'
replaceCodeLine<--method | Class '"LineWise"'
replaceCodeLine<--method | Class '"SYSargsList"'
replaceParam | Accessories function to modify the Command-line Version 1
replaceParam2 | Accessories function to modify the Command-line Version 2
replaceStep<- | Class '"SYSargsList"'
replaceStep<--method | Class '"SYSargsList"'
results | SYSargs accessor methods
results-method | Class '"SYSargs"'
results-methods | SYSargs accessor methods
returnRPKM | RPKM Normalization
rmdPath | Class '"LineWise"'
rmdPath-method | Class '"LineWise"'
runCommandline | Execute SYSargs and SYSargs2
runDiff | Differential abundance analysis for many range sets
runInfo | Class '"SYSargsList"'
runInfo-method | Class '"LineWise"'
runInfo-method | Class '"SYSargsList"'
runWF | Execute SYSargsList
run_DESeq2 | Runs DESeq2
run_edgeR | Runs edgeR

## -- S --

sal2bash | Translate SYSargsList back to a bash workflow
sal2rmd | Translate SYSargsList back to a workflow template Rmarkdown file
SampleName | Class '"SYSargsList"'
SampleName-method | Class '"SYSargs"'
SampleName-method | Class '"SYSargs2"'
SampleName-method | Class '"SYSargsList"'
SampleName-methods | SYSargs accessor methods
scaleRanges | Scale spliced ranges to genome coordinates
SE | Class '"SYSargsList"'
SE-method | Class '"SYSargsList"'
seeFastq | Quality reports for FASTQ files
seeFastqPlot | Quality reports for FASTQ files
setlist | Set Intersect and Venn Diagram Functions
setlist-method | Class '"INTERSECTset"'
setlist-method | Class '"VENNset"'
setlist-methods | Set Intersect and Venn Diagram Functions
show-method | Class '"EnvModules"'
show-method | Class '"INTERSECTset"'
show-method | Class '"LineWise"'
show-method | Class '"SYSargs"'
show-method | Class '"SYSargs2"'
show-method | Class '"SYSargsList"'
show-method | Class '"VENNset"'
show-method | Class '"catDB"'
showDF | Create an HTML table using DT package with fixed columns
software | SYSargs accessor methods
software-method | Class '"SYSargs"'
software-methods | SYSargs accessor methods
SPRproject | Workflow Project Initiation
status | Class '"SYSargs2"'
status-method | Class '"LineWise"'
status-method | Class '"SYSargs2"'
statusWF | Class '"SYSargsList"'
statusWF-method | Class '"SYSargsList"'
stepName | Class '"SYSargsList"'
stepName-method | Class '"LineWise"'
stepName-method | Class '"SYSargsList"'
stepsWF | Class '"SYSargsList"'
stepsWF-method | Class '"SYSargsList"'
subset | Class '"SYSargsList"'
subset-method | Class '"SYSargsList"'
subsetParam | Accessories function to modify the Command-line Version 1
subsetWF | Subsetting SYSargs2 class slots
symLink2bam | Symbolic links for IGV
sysargs | SYSargs accessor methods
SYSargs-class | Class '"SYSargs"'
sysargs-method | Class '"SYSargs"'
sysargs-methods | SYSargs accessor methods
sysargs2 | Class '"SYSargs2"'
SYSargs2-class | Class '"SYSargs2"'
sysargs2-method | Class '"SYSargs2"'
SYSargsList | SYSargsList Constructor
sysargslist | Class '"SYSargsList"'
SYSargsList-class | Class '"SYSargsList"'
sysargslist-method | Class '"SYSargsList"'
systemArgs | Constructs SYSargs object from param and targets files

## -- T --

targets | Class '"SYSargs2"'
targets-method | Class '"SYSargs2"'
targets.as.df | Convert targets to list or data.frame
targets.as.list | Convert targets to list or data.frame
targetsheader | Class '"SYSargsList"'
targetsheader-method | Class '"SYSargs"'
targetsheader-method | Class '"SYSargs2"'
targetsheader-method | Class '"SYSargsList"'
targetsheader-methods | SYSargs accessor methods
targetsin | SYSargs accessor methods
targetsin-method | Class '"SYSargs"'
targetsin-methods | SYSargs accessor methods
targetsout | SYSargs accessor methods
targetsout-method | Class '"SYSargs"'
targetsout-methods | SYSargs accessor methods
targetsWF | Class '"SYSargsList"'
targetsWF-method | Class '"SYSargsList"'
targets_connection | Class '"SYSargsList"'
targets_connection-method | Class '"SYSargsList"'
trimbatch | Genome read coverage by transcript models
tryCL | Collect information about the third-party software
tryCMD | Collect information about the third-party software
tryPath | Validation of the files or directories

## -- U --

updateColumn<- | Class '"SYSargsList"'
updateColumn<--method | Class '"SYSargsList"'
updateWF | Constructs SYSargs2 object from CWL param and targets files

## -- V --

variantReport | Generate Variant Report
varSummary | Generate Variant Report
vennlist | Set Intersect and Venn Diagram Functions
vennlist-method | Class '"VENNset"'
vennlist-methods | Set Intersect and Venn Diagram Functions
vennPlot | Plot 2-5 way Venn diagrams
VENNset-class | Class '"VENNset"'
viewEnvir | Class '"SYSargsList"'
viewEnvir-method | Class '"SYSargsList"'

## -- W --

wf | Class '"SYSargs2"'
wf-method | Class '"SYSargs2"'
writeParamFiles | createParam
writeTargets | Write updated targets out to file from 'SYSargsList'
writeTargetsout | Write updated targets out to file
writeTargetsRef | Generate targets file with reference
write_SYSargsList | Writeout SYSargsList object

## -- Y --

yamlinput | Class '"SYSargsList"'
yamlinput-method | Class '"SYSargs2"'
yamlinput-method | Class '"SYSargsList"'
yamlinput<- | Class '"SYSargsList"'
yamlinput<--method | Class '"SYSargs2"'
yamlinput<--method | Class '"SYSargsList"'

## -- misc --

$-method | Class '"EnvModules"'
$-method | Class '"LineWise"'
$-method | Class '"SYSargs2"'
$-method | Class '"SYSargsList"'
[-method | Class '"EnvModules"'
[-method | Class '"LineWise"'
[-method | Class '"SYSargs"'
[-method | Class '"SYSargs2"'
[-method | Class '"SYSargsList"'
[[-method | Class '"EnvModules"'
[[-method | Class '"LineWise"'
[[-method | Class '"SYSargs2"'
[[-method | Class '"SYSargsList"'
[[<--method | Class '"EnvModules"'
[[<--method | Class '"LineWise"'
[[<--method | Class '"SYSargs2"'
[[<--method | Class '"SYSargsList"'