systemPipeR: NGS workflow and report generation environment

Documentation for package ‘systemPipeR’ version 2.4.0

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

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"'