systemPipeR: NGS workflow and report generation environment

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Documentation for package ‘systemPipeR’ version 1.26.3

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A B C D E F G I L M N O P Q R S T 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
alignStats Alignment statistics
appendParam Accessories function to modify the Command-line
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 '"SYSargs2"'
baseCommand-method Class '"SYSargs2"'

-- 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.output Checking if the output files exist
clt Class '"SYSargs2"'
clt-method Class '"SYSargs2"'
clusterRun Submit command-line tools to cluster
cmdlist Class '"SYSargs2"'
cmdlist-method Class '"SYSargs2"'
cmdlist-method Class '"SYSargsList"'
cmdToCwl Class '"SYSargs2"'
cmdToCwl-method Class '"SYSargs2"'
codeSteps-method Class '"SYSargsList"'
coerce-method Class '"EnvModules"'
coerce-method Class '"INTERSECTset"'
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
cores SYSargs accessor methods
cores-method Class '"SYSargs"'
cores-methods SYSargs accessor methods
countRangeset Read counting for several range sets
createParamFiles createParamFiles
cwlfiles Class '"SYSargs2"'
cwlfiles-method Class '"SYSargs2"'

-- D --

default_modules-method Class '"EnvModules"'
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
filterDEGs Filter and plot DEG results
filterVars Filter VCF files

-- G --

genFeatures Generate feature ranges from TxDb
getQsubargs Arguments for qsub
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
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
initProject Workflow Project Initiation
initWF Workflow Project Initiation
input Class '"SYSargs2"'
input-method Class '"SYSargs2"'
inputvars Class '"SYSargs2"'
inputvars-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 '"SYSargs"'
length-method Class '"SYSargs2"'
length-method Class '"SYSargsList"'
length-method Class '"VENNset"'
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 SYSargs accessor methods
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 '"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 Graphviz Plot Workflow
predORF Predict ORFs
preprocessReads Run custom read preprocessing functions
printParam Accessories function to modify the Command-line
projectWF Class '"SYSargsList"'
projectWF-method Class '"SYSargsList"'

-- Q --

qsubRun Submit command-line tools to cluster

-- R --

readComp Import sample comparisons from targets file
reference SYSargs accessor methods
reference-method Class '"SYSargs"'
reference-methods SYSargs accessor methods
renameParam Accessories function to modify the Command-line
renameStep<- Class '"SYSargsList"'
renameStep<--method Class '"SYSargsList"'
renderReport Render RMarkdown Report
renderWF Populate all the command-line in an 'SYSargs2' object
replaceParam Accessories function to modify the Command-line
replaceStep<- Class '"SYSargsList"'
replaceStep<--method Class '"SYSargsList"'
results SYSargs accessor methods
results-method Class '"SYSargs"'
results-methods SYSargs accessor methods
returnRPKM RPKM Normalization
runCommandline Execute SYSargs and SYSargs2
runDiff Differential abundance analysis for many range sets
runWF Execute SYSargsList
run_DESeq2 Runs DESeq2
run_edgeR Runs edgeR

-- S --

SampleName SYSargs accessor methods
SampleName-method Class '"SYSargs"'
SampleName-methods SYSargs accessor methods
scaleRanges Scale spliced ranges to genome coordinates
seeFastq Quality reports for FASTQ files
seeFastqPlot Quality reports for FASTQ files
SEobj Class '"SYSargsList"'
SEobj-method Class '"SYSargsList"'
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 '"SYSargs"'
show-method Class '"SYSargs2"'
show-method Class '"SYSargsList"'
show-method Class '"VENNset"'
show-method Class '"catDB"'
software SYSargs accessor methods
software-method Class '"SYSargs"'
software-methods SYSargs accessor methods
sprconfig Class '"SYSargsList"'
sprconfig-method Class '"SYSargsList"'
SPRdata SPRdata
SPRproject Workflow Project Initiation
statusWF Class '"SYSargsList"'
statusWF-method Class '"SYSargsList"'
stepsWF Class '"SYSargsList"'
stepsWF-method Class '"SYSargsList"'
subsetParam Accessories function to modify the Command-line
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
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 list to data.frame
targetsheader SYSargs accessor methods
targetsheader-method Class '"SYSargs"'
targetsheader-method Class '"SYSargs2"'
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"'
tryCL Collect information about the third-party software
tryPath Validation of the files or directories

-- 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"'

-- W --

wf Class '"SYSargs2"'
wf-method Class '"SYSargs2"'
writeParamFiles createParamFiles
writeTargetsout Write updated targets out to file
writeTargetsRef Generate targets file with reference

-- Y --

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

-- misc --

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