systemPipeR: NGS workflow and report generation environment

Documentation for package ‘systemPipeR’ version 1.22.0

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

-- A --

alignStats	Alignment statistics
as.list-method	Class '"INTERSECTset"'
as.list-method	Class '"VENNset"'

-- 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
clt	SYSargs2 accessor methods
clt-method	Class '"SYSargs2"'
clt-methods	SYSargs2 accessor methods
clusterRun	Submit command-line tools to cluster
cmdlist	SYSargs2 accessor methods
cmdlist-method	Class '"SYSargs2"'
cmdlist-methods	SYSargs2 accessor methods
codeSteps	SYSargsList accessor methods
codeSteps-method	Class '"SYSargsList"'
codeSteps-methods	SYSargsList accessor methods
coerce-method	Class '"INTERSECTset"'
coerce-method	Class '"SYSargs"'
coerce-method	Class '"SYSargs2"'
coerce-method	Deprecated '"SYSargs2Pipe"' Class
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
createWF	Constructs SYSargs2 object and creates CWL param files
cwlfiles	SYSargs2 accessor methods
cwlfiles-method	Class '"SYSargs2"'
cwlfiles-methods	SYSargs2 accessor methods

-- D --

dataWF	SYSargsList accessor methods
dataWF-method	Class '"SYSargsList"'
dataWF-methods	SYSargsList accessor methods

-- E --

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	SYSargs2 accessor methods
input-method	Class '"SYSargs2"'
input-methods	SYSargs2 accessor methods
inputvars	SYSargs2 accessor methods
inputvars-method	Class '"SYSargs2"'
inputvars-methods	SYSargs2 accessor methods
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	Deprecated '"SYSargs2Pipe"' Class
length-method	Class '"SYSargsList"'
length-method	Class '"VENNset"'
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
modulelist	Interface to module system
moduleload	Interface to module system
modules	SYSargs accessor methods
modules-method	Class '"SYSargs"'
modules-method	Class '"SYSargs2"'
modules-methods	SYSargs accessor methods

-- N --

names-method	Class '"INTERSECTset"'
names-method	Class '"SYSargs"'
names-method	Class '"SYSargs2"'
names-method	Deprecated '"SYSargs2Pipe"' Class
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
outpaths	SYSargs accessor methods
outpaths-method	Class '"SYSargs"'
outpaths-methods	SYSargs accessor methods
output	SYSargs2 accessor methods
output-method	Class '"SYSargs2"'
output-methods	SYSargs2 accessor methods
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
projectWF	SYSargsList accessor methods
projectWF-method	Class '"SYSargsList"'
projectWF-methods	SYSargsList accessor methods

-- 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
renderReport	Render RMarkdown Report
renderWF	Populate all the command-line in an 'SYSargs2' object
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
run_track	Deprecated 'run_track' functions

-- 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
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 '"INTERSECTset"'
show-method	Class '"SYSargs"'
show-method	Class '"SYSargs2"'
show-method	Deprecated '"SYSargs2Pipe"' Class
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
statusWF	SYSargsList accessor methods
statusWF-method	Class '"SYSargsList"'
statusWF-methods	SYSargsList accessor methods
stepsWF	SYSargsList accessor methods
stepsWF-method	Class '"SYSargsList"'
stepsWF-methods	SYSargsList accessor methods
subsetWF	Subsetting SYSargs2 class slots
summaryWF	Deprecated '"SYSargs2Pipe"' accessor methods
summaryWF-method	Deprecated '"SYSargs2Pipe"' Class
summaryWF-method	Class '"SYSargsList"'
summaryWF-methods	Deprecated '"SYSargs2Pipe"' accessor methods
symLink2bam	Symbolic links for IGV
sysargs	SYSargs accessor methods
SYSargs-class	Class '"SYSargs"'
sysargs-method	Class '"SYSargs"'
sysargs-methods	SYSargs accessor methods
sysargs2	SYSargs2 accessor methods
SYSargs2-class	Class '"SYSargs2"'
sysargs2-method	Class '"SYSargs2"'
sysargs2-method	SYSargs2 accessor methods
SYSargs2Pipe-class	Deprecated '"SYSargs2Pipe"' Class
SYSargs2Pipe-method	Deprecated '"SYSargs2Pipe"' accessor methods
SYSargs2Pipe_ls	Deprecated '"SYSargs2Pipe"' accessor methods
SYSargs2Pipe_ls-method	Deprecated '"SYSargs2Pipe"' Class
SYSargs2_steps	SYSargsList accessor methods
SYSargs2_steps-method	Class '"SYSargsList"'
SYSargs2_steps-methods	SYSargsList accessor methods
sysargslist	SYSargsList accessor methods
SYSargsList-class	Class '"SYSargsList"'
sysargslist-method	Class '"SYSargsList"'
sysargslist-method	SYSargsList accessor methods
sysconfig	SYSargsList accessor methods
sysconfig-method	Class '"SYSargsList"'
sysconfig-methods	SYSargsList accessor methods
SYSproject	Workflow Project Initiation
systemArgs	Constructs SYSargs object from param and targets files

-- T --

targets	SYSargs2 accessor methods
targets-method	Class '"SYSargs2"'
targets-methods	SYSargs2 accessor methods
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
track	Deprecated '"SYSargs2Pipe"' accessor methods
track-method	Deprecated '"SYSargs2Pipe"' Class
track-methods	Deprecated '"SYSargs2Pipe"' accessor methods
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	SYSargs2 accessor methods
wf-method	Class '"SYSargs2"'
wf-methods	SYSargs2 accessor methods
WF_steps	Deprecated '"SYSargs2Pipe"' accessor methods
WF_steps-method	Deprecated '"SYSargs2Pipe"' Class
WF_steps-methods	Deprecated '"SYSargs2Pipe"' accessor methods
writeTargetsout	Write updated targets out to file
writeTargetsRef	Generate targets file with reference

-- Y --

yamlinput	SYSargs2 accessor methods
yamlinput-method	Class '"SYSargs2"'
yamlinput-methods	SYSargs2 accessor methods

-- misc --

$-method	Class '"SYSargs2"'
$-method	Deprecated '"SYSargs2Pipe"' Class
$-method	Class '"SYSargsList"'
[-method	Class '"SYSargs"'
[-method	Class '"SYSargs2"'
[-method	Deprecated '"SYSargs2Pipe"' Class
[-method	Class '"SYSargsList"'
[[-method	Class '"SYSargs2"'
[[-method	Deprecated '"SYSargs2Pipe"' Class
[[-method	Class '"SYSargsList"'
[[<--method	Class '"SYSargs2"'
[[<--method	Deprecated '"SYSargs2Pipe"' Class
[[<--method	Class '"SYSargsList"'