systemPipeR: Workflow Environment for Data Analysis and Report Generation


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Documentation for package ‘systemPipeR’ version 2.15.0

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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 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"'
listCmdModules List/check the existence of command-line tools of a workflow
listCmdTools List/check the existence of command-line tools of a workflow
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"'
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"'