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HTSeqGenie (version 3.18.0)
A NGS analysis pipeline.
Description
Libraries to perform NGS analysis.
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Version
4.2.0
3.20.0
3.18.0
3.16.1
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Version
3.18.0
License
Artistic-2.0
Maintainer
Jens Reeder
Last Published
June 10th, 2014
Functions in HTSeqGenie (3.18.0)
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buildShortReadReports
Build a ShortRead report
buildTallyParam
Build tally parameters
consolidateByRead
Consolidate Paired-End Alignments by Read Names
countFeatures
Count RNA-Seq Pipeline Genomic Features
excludeVariantsByRegions
Filter variants by regions
FastQStreamer.getReads
Get FastQ reads from the FastQ streamer
filterByLength
Filter reads by length
filterQuality
Filter reads by quality
getConfig.numeric
Check if a config parameter is a numeric
getConfig.vector
Return values of a config variable as vector
hashVector
Hashing function for vector
HTSeqGenie
Package overview
isFirstFragment
Does a SAM flag indicate the first fragment
isSparse
isSparse
makeRandomSreads
Generate a couple if random ShortReadQ, intended for testing
markDuplicates
markDuplicates
mergeSummaryAlignment
Merge summary alignments
mergePreprocessReads
Merge after preprocessReads
readRNASeqEnds
Read Paired End Bam Files
readInputFiles
Read FastQ input files
setUpDirs
Create output directory and subdirectories for sequencing pipeline analysis outputs
setChunkDir
Set the base directory for the chunks
trimReads
Trim/truncate a set of reads
trimTailsByQuality
Trim off low quality tail
analyzeVariants
Calculate and process Variants
bamCountUniqueReads
Uniquely count number of reads in bam file
calculateCoverage
Calculate read coverage
calculateTargetLengths
Plot target length for paired end
detectQualityInFASTQFile
Detect quality protocol from a FASTQ file
detectRRNA
Detect rRNA Contamination in Reads
getBams
Get bam files of a pipeline run
hashVariants
Hashing function for variants
hashCoverage
Hashing function for coverage
getAdapterSeqs
Read list of Illumina adapter seqs from package data
initPipelineFromSaveDir
Init Pipeline environment from previous run
loginfo
Log info using the logging package
isAboveQualityThresh
Check for high quality reads
parseDCF
Read and parse a configuration file
logerror
Log info using the logging package
parseSummaries
parse summary files from save dirs
getNumberOfReadsInFASTQFile
Count reads in Fastq file
computeBamStats
Compute record statistics from a bam file
computeCoverage
Compute the coverage vector given a bamfile
initDirs
Set up NGS output dir
getNumericVectorDataFromFile
Load data as numerical values
initLog
Initialize the logger
isAdapter
Detect adapter contamination
isConfig
Test the presence of the parameter in the current config
mergeCoverage
Merge coverage files
mergeLanes
Merge input lanes
plotDF
Make continuous plots of distribution function
runPipeline
Run the NGS analysis pipeline
preprocessReads
Pipeline preprocessing
runAlignment
Runs the read alignment step of the pipeline
writeConfig
Write a config file
writeFastQFiles
Write reads to file
rpkm
Calculate RPKM
resource
Reload package source code
safeExecute
Execute function in try catch with trace function
safe.yield
Overloaded yield(...) method catching truncated exceptions for FastqStreamer
updateConfig
Update the existing config
vcfStat
Compute stats on a VCF file
writeFeatureCountsHTML
writeFeatureCountsHTML
writeGenomicFeaturesReport
Generate pipeline report
alignReads
Align reads against genome
alignReadsChunk
Genomic alignment
countGenomicFeaturesChunk
Count reads by genomic Feature
countGenomicFeatures
Count overlaps with genomic features
getObjectFilename
Get a filename given a directory and the object name
findVariantFile
Get a vcf filename given a HTSeqGenie directory
gatk
gatk
getPackageFile
Get a package file
getTabDataFromFile
Load tabular data from the NGS pipeline result directory
getTraceback
Get traceback from tryKeepTraceback()
listIterator.init
Create a iterator on a list
markDups
markDups
listIterator.next
Get reads from the listIterator
mergeAlignReads
Merge after alignReads
realignIndels
realignIndels
realignIndelsGATK
Realign indels via GATK
saveWithID
Save an R object
sclapply
Scheduled parallel processing
setupTestFramework
setup test framework
statCountFeatures
Compute statistics on count features
writePreprocessAlignHTML
writePreprocessAlignHTML
writePreprocessAlignReport
Generate Pipeline Report
buildTP53FastaGenome
buildTP53FastaGenome
checkGATKJar
Check for the GATK jar file
buildTP53GenomeTemplate
buildTP53GenomeTemplate
checkPicardJar
checkPicardJar
createTmpDir
Create a random directory with prefix in R temp dir
detectAdapterContam
Detect sequencing adapter contamination
getConfig
Get a configuration parameter
getConfig.logical
Check if a config parameter has a logical value
getEndNumber
Get Read End Number
initPipelineFromConfig
Init pipeline environment
getMemoryUsage
Returns memory usage in bytes
initLogger
Init loggers
buildGenomicFeaturesFromTxDb
Build genomic features from a TxDb object
callVariantsGATK
Variant calling via GATK
buildConfig
Build a configuration file based on a list of parameters
checkConfig
Check configuration
loadConfig
Load configuration file
logdebug
Log debug using the logging package
makeDir
Make a directory after performing an existence check
logwarn
Log warning using the logging package
processChunks
Process chunk in the pipeline framework
preprocessReadsChunk
Preprocess a chunk
FastQStreamer.init
Open a streaming connection to a FastQ file
getChunkDirs
Get the list of chunk directories
getConfig.integer
Check if a config parameter is an integer
getRandomAlignCutoff
Estimate an adapter alignment cutoff score
FastQStreamer.release
Close the FastQStreamer
getRRNAIds
Detect reads that look like rRNA
plotDepthByStrand
Plot Read Depth of Variants by Strand
picard
picard
runPipelineConfig
Run the NGS analysis pipeline
runPreprocessReads
Run the preprocesing steps of the pipeline
truncateReads
Trim/truncate a set of reads
tryKeepTraceback
Wrapper around try-catch
relativeBarPlot
Make relative bar plots
removeChunkDir
Remove chunk directories
safeGetObject
Safely load a R data file
safeUnlink
safeUnlink
traceMem
Show memory usage
TP53GenomicFeatures
Demo genomic features around the TP53 gene
writeSummary
Write HTML summary
writeVCF
writeVCF
wrap.callVariants
Variant calling
writeAudit
Write Session information