systemPipeR: NGS workflow and report generation environment


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Documentation for package ‘systemPipeR’ version 1.18.2

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A C 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
coerce-method Class '"INTERSECTset"'
coerce-method Class '"SYSargs"'
coerce-method Class '"SYSargs2"'
coerce-method Class '"SYSargs2Pipe"'
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
cores SYSargs accessor methods
cores-method Class '"SYSargs"'
cores-methods SYSargs accessor methods
countRangeset Read counting for several range sets
cwlfiles SYSargs2 accessor methods
cwlfiles-method Class '"SYSargs2"'
cwlfiles-methods SYSargs2 accessor methods

-- 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
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 Class '"SYSargs2Pipe"'
length-method Class '"VENNset"'
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 Class '"SYSargs2Pipe"'
names-method Class '"VENNset"'
names-method Class '"catDB"'

-- O --

olBarplot Bar plot for intersect sets
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
predORF Predict ORFs
preprocessReads Run custom read preprocessing functions

-- 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
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
run_DESeq2 Runs DESeq2
run_edgeR Runs edgeR
run_track Keep track of the all 'SYSargs2' object

-- 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 Class '"SYSargs2Pipe"'
show-method Class '"VENNset"'
show-method Class '"catDB"'
software SYSargs accessor methods
software-method Class '"SYSargs"'
software-methods SYSargs accessor methods
subsetWF Subsetting SYSargs2 class slots
summaryWF SYSargs2Pipe accessor methods
summaryWF-method Class '"SYSargs2Pipe"'
summaryWF-methods 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-class Class '"SYSargs2"'
SYSargs2list SYSargs2 accessor methods
SYSargs2list-method Class '"SYSargs2"'
SYSargs2list-method SYSargs2 accessor methods
SYSargs2Pipe-class Class '"SYSargs2Pipe"'
SYSargs2Pipe-method SYSargs2Pipe accessor methods
SYSargs2Pipe_ls SYSargs2Pipe accessor methods
SYSargs2Pipe_ls-method Class '"SYSargs2Pipe"'
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 SYSargs2Pipe accessor methods
track-method Class '"SYSargs2Pipe"'
track-methods SYSargs2Pipe accessor methods

-- 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 SYSargs2Pipe accessor methods
WF_steps-method Class '"SYSargs2Pipe"'
WF_steps-methods 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 Class '"SYSargs2Pipe"'
[-method Class '"SYSargs"'
[-method Class '"SYSargs2"'
[-method Class '"SYSargs2Pipe"'
[[-method Class '"SYSargs2"'
[[-method Class '"SYSargs2Pipe"'
[[<--method Class '"SYSargs2"'
[[<--method Class '"SYSargs2Pipe"'