Man pages for HTSeqGenie
A NGS analysis pipeline.

alignReadsAlign reads against genome
alignReadsChunkGenomic alignment
analyzeVariantsCalculate and process Variants
annotateVariantsAnnotate variants via vep
bamCountUniqueReadsUniquely count number of reads in bam file
buildConfigBuild a configuration file based on a list of parameters
buildGenomicFeaturesFromTxDbBuild genomic features from a TxDb object
buildShortReadReportsBuild a ShortRead report
buildTallyParamBuild tally parameters
buildTP53FastaGenomebuildTP53FastaGenome
buildTP53GenomeTemplatebuildTP53GenomeTemplate
calculateCoverageCalculate read coverage
calculateTargetLengthsPlot target length for paired end
callVariantsGATKVariant calling via GATK
checkConfigCheck configuration
checkGATKJarCheck for the GATK jar file
checkPicardJarcheckPicardJar
computeBamStatsCompute record statistics from a bam file
computeCoverageCompute the coverage vector given a bamfile
countFeaturesCount RNA-Seq Pipeline Genomic Features
countGenomicFeaturesCount overlaps with genomic features
countGenomicFeaturesChunkCount reads by genomic Feature
createTmpDirCreate a random directory with prefix in R temp dir
detectAdapterContamDetect sequencing adapter contamination
detectQualityInFASTQFileDetect quality protocol from a FASTQ file
detectRRNADetect rRNA Contamination in Reads
excludeVariantsByRegionsFilter variants by regions
FastQStreamer.getReadsGet FastQ reads from the FastQ streamer
FastQStreamer.initOpen a streaming connection to a FastQ file
FastQStreamer.releaseClose the FastQStreamer
filterByLengthFilter reads by length
filterQualityFilter reads by quality
findVariantFileGet a vcf filename given a HTSeqGenie directory
gatkgatk
generateSingleGeneDERsgenerateSingleGeneDERs
getAdapterSeqsRead list of Illumina adapter seqs from package data
getBamsGet bam files of a pipeline run
getChunkDirsGet the list of chunk directories
getConfigGet a configuration parameter
getConfig.integerCheck if a config parameter is an integer
getConfig.logicalCheck if a config parameter has a logical value
getConfig.numericCheck if a config parameter is a numeric
getConfig.vectorReturn values of a config variable as vector
getEndNumberGet Read End Number
getMemoryUsageReturns memory usage in bytes
getNumberOfReadsInFASTQFileCount reads in Fastq file
getNumericVectorDataFromFileLoad data as numerical values
getObjectFilenameGet a filename given a directory and the object name
getPackageFileGet a package file
getRandomAlignCutoffEstimate an adapter alignment cutoff score
getRRNAIdsDetect reads that look like rRNA
getTabDataFromFileLoad tabular data from the NGS pipeline result directory
getTracebackGet traceback from tryKeepTraceback()
hashCoverageHashing function for coverage
hashVariantsHashing function for variants
hashVectorHashing function for vector
HTSeqGeniePackage overview
initDirsSet up NGS output dir
initLogInitialize the logger
initLoggerInit loggers
initPipelineFromConfigInit pipeline environment
initPipelineFromSaveDirInit Pipeline environment from previous run
isAboveQualityThreshCheck for high quality reads
isAdapterDetect adapter contamination
isConfigTest the presence of the parameter in the current config
isFirstFragmentDoes a SAM flag indicate the first fragment
isSparseisSparse
listIterator.initCreate a iterator on a list
listIterator.nextGet reads from the listIterator
loadConfigLoad configuration file
logdebugLog debug using the logging package
logerrorLog info using the logging package
loginfoLog info using the logging package
logwarnLog warning using the logging package
makeDirMake a directory after performing an existence check
makeRandomSreadsGenerate a couple if random ShortReadQ, intended for testing
markDuplicatesmarkDuplicates
markDupsmarkDups
mergeAlignReadsMerge after alignReads
mergeCoverageMerge coverage files
mergeLanesMerge input lanes
mergePreprocessReadsMerge after preprocessReads
mergeSummaryAlignmentMerge summary alignments
parseDCFRead and parse a configuration file
parseSummariesparse summary files from save dirs
picardpicard
plotDFMake continuous plots of distribution function
preprocessReadsPipeline preprocessing
preprocessReadsChunkPreprocess a chunk
processChunksProcess chunk in the pipeline framework
readInputFilesRead FastQ input files
readRNASeqEndsRead single/paired End Bam Files
realignIndelsrealignIndels
realignIndelsGATKRealign indels via GATK
relativeBarPlotMake relative bar plots
removeChunkDirRemove chunk directories
resourceReload package source code
rpkmCalculate RPKM
runAlignmentRuns the read alignment step of the pipeline
runPipelineRun the NGS analysis pipeline
runPipelineConfigRun the NGS analysis pipeline
runPreprocessReadsRun the preprocesing steps of the pipeline
safeExecuteExecute function in try catch with trace function
safeGetObjectSafely load a R data file
safeUnlinksafeUnlink
safe.yieldOverloaded yield(...) method catching truncated exceptions...
saveWithIDSave an R object
sclapplyScheduled parallel processing
setChunkDirSet the base directory for the chunks
setUpDirsCreate output directory and subdirectories for sequencing...
setupTestFrameworksetup test framework
statCountFeaturesCompute statistics on count features
TP53GenomicFeaturesDemo genomic features around the TP53 gene
traceMemShow memory usage
trimReadsTrim/truncate a set of reads
trimTailsByQualityTrim off low quality tail
truncateReadsTrim/truncate a set of reads
tryKeepTracebackWrapper around try-catch
updateConfigUpdate the existing config
vcfStatCompute stats on a VCF file
wrap.callVariantsVariant calling
writeAuditWrite Session information
writeConfigWrite a config file
writeFastQFilesWrite reads to file
writeFeatureCountsHTMLwriteFeatureCountsHTML
writeGenomicFeaturesReportGenerate pipeline report
writePreprocessAlignHTMLwritePreprocessAlignHTML
writePreprocessAlignReportGenerate Pipeline Report
writeSummaryWrite HTML summary
writeVCFwriteVCF
HTSeqGenie documentation built on Oct. 31, 2019, 2:14 a.m.