Man pages for HTSeqGenie
A NGS analysis pipeline.

alignReads	Align reads against genome
alignReadsChunk	Genomic alignment
analyzeVariants	Calculate and process Variants
annotateVariants	Annotate variants via vep
bamCountUniqueReads	Uniquely count number of reads in bam file
buildConfig	Build a configuration file based on a list of parameters
buildGenomicFeaturesFromTxDb	Build genomic features from a TxDb object
buildShortReadReports	Build a ShortRead report
buildTallyParam	Build tally parameters
buildTP53FastaGenome	buildTP53FastaGenome
buildTP53GenomeTemplate	buildTP53GenomeTemplate
calculateCoverage	Calculate read coverage
calculateTargetLengths	Plot target length for paired end
callVariantsGATK	Variant calling via GATK
checkConfig	Check configuration
checkGATKJar	Check for the GATK jar file
checkPicardJar	checkPicardJar
computeBamStats	Compute record statistics from a bam file
computeCoverage	Compute the coverage vector given a bamfile
countFeatures	Count RNA-Seq Pipeline Genomic Features
countGenomicFeatures	Count overlaps with genomic features
countGenomicFeaturesChunk	Count reads by genomic Feature
createTmpDir	Create a random directory with prefix in R temp dir
detectAdapterContam	Detect sequencing adapter contamination
detectQualityInFASTQFile	Detect quality protocol from a FASTQ file
detectRRNA	Detect rRNA Contamination in Reads
excludeVariantsByRegions	Filter variants by regions
FastQStreamer.getReads	Get FastQ reads from the FastQ streamer
FastQStreamer.init	Open a streaming connection to a FastQ file
FastQStreamer.release	Close the FastQStreamer
filterByLength	Filter reads by length
filterQuality	Filter reads by quality
findVariantFile	Get a vcf filename given a HTSeqGenie directory
gatk	gatk
generateSingleGeneDERs	generateSingleGeneDERs
getAdapterSeqs	Read list of Illumina adapter seqs from package data
getBams	Get bam files of a pipeline run
getChunkDirs	Get the list of chunk directories
getConfig	Get a configuration parameter
getConfig.integer	Check if a config parameter is an integer
getConfig.logical	Check if a config parameter has a logical value
getConfig.numeric	Check if a config parameter is a numeric
getConfig.vector	Return values of a config variable as vector
getEndNumber	Get Read End Number
getMemoryUsage	Returns memory usage in bytes
getNumberOfReadsInFASTQFile	Count reads in Fastq file
getNumericVectorDataFromFile	Load data as numerical values
getObjectFilename	Get a filename given a directory and the object name
getPackageFile	Get a package file
getRandomAlignCutoff	Estimate an adapter alignment cutoff score
getRRNAIds	Detect reads that look like rRNA
getTabDataFromFile	Load tabular data from the NGS pipeline result directory
getTraceback	Get traceback from tryKeepTraceback()
hashCoverage	Hashing function for coverage
hashVariants	Hashing function for variants
hashVector	Hashing function for vector
HTSeqGenie	Package overview
initDirs	Set up NGS output dir
initLog	Initialize the logger
initLogger	Init loggers
initPipelineFromConfig	Init pipeline environment
initPipelineFromSaveDir	Init Pipeline environment from previous run
isAboveQualityThresh	Check for high quality reads
isAdapter	Detect adapter contamination
isConfig	Test the presence of the parameter in the current config
isFirstFragment	Does a SAM flag indicate the first fragment
isSparse	isSparse
listIterator.init	Create a iterator on a list
listIterator.next	Get reads from the listIterator
loadConfig	Load configuration file
logdebug	Log debug using the logging package
logerror	Log info using the logging package
loginfo	Log info using the logging package
logwarn	Log warning using the logging package
makeDir	Make a directory after performing an existence check
makeRandomSreads	Generate a couple if random ShortReadQ, intended for testing
markDuplicates	markDuplicates
markDups	markDups
mergeAlignReads	Merge after alignReads
mergeCoverage	Merge coverage files
mergeLanes	Merge input lanes
mergePreprocessReads	Merge after preprocessReads
mergeSummaryAlignment	Merge summary alignments
parseDCF	Read and parse a configuration file
parseSummaries	parse summary files from save dirs
picard	picard
plotDF	Make continuous plots of distribution function
preprocessReads	Pipeline preprocessing
preprocessReadsChunk	Preprocess a chunk
processChunks	Process chunk in the pipeline framework
readInputFiles	Read FastQ input files
readRNASeqEnds	Read single/paired End Bam Files
realignIndels	realignIndels
realignIndelsGATK	Realign indels via GATK
relativeBarPlot	Make relative bar plots
removeChunkDir	Remove chunk directories
resource	Reload package source code
rpkm	Calculate RPKM
runAlignment	Runs the read alignment step of the pipeline
runPipeline	Run the NGS analysis pipeline
runPipelineConfig	Run the NGS analysis pipeline
runPreprocessReads	Run the preprocesing steps of the pipeline
safeExecute	Execute function in try catch with trace function
safeGetObject	Safely load a R data file
safeUnlink	safeUnlink
safe.yield	Overloaded yield(...) method catching truncated exceptions...
saveWithID	Save an R object
sclapply	Scheduled parallel processing
setChunkDir	Set the base directory for the chunks
setUpDirs	Create output directory and subdirectories for sequencing...
setupTestFramework	setup test framework
statCountFeatures	Compute statistics on count features
TP53GenomicFeatures	Demo genomic features around the TP53 gene
traceMem	Show memory usage
trimReads	Trim/truncate a set of reads
trimTailsByQuality	Trim off low quality tail
truncateReads	Trim/truncate a set of reads
tryKeepTraceback	Wrapper around try-catch
updateConfig	Update the existing config
vcfStat	Compute stats on a VCF file
wrap.callVariants	Variant calling
writeAudit	Write Session information
writeConfig	Write a config file
writeFastQFiles	Write reads to file
writeFeatureCountsHTML	writeFeatureCountsHTML
writeGenomicFeaturesReport	Generate pipeline report
writePreprocessAlignHTML	writePreprocessAlignHTML
writePreprocessAlignReport	Generate Pipeline Report
writeSummary	Write HTML summary
writeVCF	writeVCF