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