# Preprocessing of Aligned Sequences from HTS Analyses

## Documentation for package ‘Pasha’ version 0.99.21

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M N P Q R S U W misc

Pasha-package | Pasha package (Preprocessing of Aligned Sequences from HTS Analyses)

## -- A --

AlignedData | Class 'AlignedData'
AlignedData-class | Class 'AlignedData'
AnalyzeRepeat | WIG Repeat Analyzer

## -- B --

binVector | Divide a numeric vector in equal bins of signal

## -- C --

checkPairsOK | Class 'AlignedData'
checkPairsOK-method | Class 'AlignedData'
cleanNonSimplePairs | Class 'AlignedData'
cleanNonSimplePairs-method | Class 'AlignedData'
CSEMDispatch | Multiread scoring CSEM dispatch
C_binVector | Divide a numeric vector in equal bins of signal
C_elongationEstimation | Shifting the positive strand vector and compute an overlap score to estimate the optimal elongation size for the fragments
C_pileupDouble | Piling vector of double

## -- D --

dropChromosomePattern | Class 'AlignedData'
dropChromosomePattern-method | Class 'AlignedData'
dropUndefinedStrand | Class 'AlignedData'
dropUndefinedStrand-method | Class 'AlignedData'

## -- E --

elongationEstimation | Shifting the positive strand vector and compute an overlap score to estimate the optimal elongation size for the fragments
estimateElongationSize | Insert size estimation in-silico

## -- F --

filterInsertSize | Class 'AlignedData'
filterInsertSize-method | Class 'AlignedData'
filterReadSize | Class 'AlignedData'
filterReadSize-method | Class 'AlignedData'
flag | Class 'AlignedData'
flag-method | Class 'AlignedData'
flag<- | Class 'AlignedData'
flag<--method | Class 'AlignedData'

## -- G --

generatePiled | Pileup reads in a numeric vector with several piling and elongation options
getArtefactsIndexes | Identify reads implied in piles potentially considered as PCR artefacts
getOrphansIndexes | Class 'AlignedData'
getOrphansIndexes-method | Class 'AlignedData'
getStats-method | Class 'AlignedData'

## -- I --

initialize | Class 'AlignedData'
isize | Class 'AlignedData'
isize-method | Class 'AlignedData'
isize<- | Class 'AlignedData'
isize<--method | Class 'AlignedData'

## -- L --

length | Class 'AlignedData'
length-method | Class 'AlignedData'

## -- M --

mapq | Class 'AlignedData'
mapq-method | Class 'AlignedData'
mapq<- | Class 'AlignedData'
mapq<--method | Class 'AlignedData'
mergeWigs | Merge several different wig files in a unique result file
mrnm | Class 'AlignedData'
mrnm-method | Class 'AlignedData'
mrnm<- | Class 'AlignedData'
mrnm<--method | Class 'AlignedData'
multiread_CSEMDispatch | Multiread scoring CSEM dispatch
multiread_RemoveArtifact | Artifact Remover
multiread_UniformDispatch | Multiread scoring uniform dispatch

## -- N --

normalizeChrNames | Class 'AlignedData'
normalizeChrNames-method | Class 'AlignedData'
normAndSubtractWIG | Normalization and subtraction of WIG files
notAligned | Class 'AlignedData'
notAligned-method | Class 'AlignedData'
notAligned<- | Class 'AlignedData'
notAligned<--method | Class 'AlignedData'

## -- P --

pairedEnds | Class 'AlignedData'
pairedEnds-method | Class 'AlignedData'
pairedEnds<- | Class 'AlignedData'
pairedEnds<--method | Class 'AlignedData'
Pasha | Pasha package (Preprocessing of Aligned Sequences from HTS Analyses)
pileupDouble | Piling vector of double
plotReadsRepartitionAnnotations | Graphical information about reads and annotations repartition
position | Class 'AlignedData'
position-method | Class 'AlignedData'
position<- | Class 'AlignedData'
position<--method | Class 'AlignedData'
processPipeline | A pipeline to accurately transform aligned reads to genomic enrichment scores

## -- Q --

qwidth | Class 'AlignedData'
qwidth-method | Class 'AlignedData'
qwidth<- | Class 'AlignedData'
qwidth<--method | Class 'AlignedData'

## -- R --

readAlignedData | Class 'AlignedData'
readID | Class 'AlignedData'
readID-method | Class 'AlignedData'
readID<- | Class 'AlignedData'
readID<--method | Class 'AlignedData'
readMultipleAlignedData | Class 'AlignedData'
readWIG | Read and Write genomic WIG (fixed step) files
RemoveArtifact | Artifact Remover

## -- S --

seqnames | Class 'AlignedData'
seqnames-method | Class 'AlignedData'
seqnames<- | Class 'AlignedData'
seqnames<--method | Class 'AlignedData'
sortByPairs | Class 'AlignedData'
sortByPairs-method | Class 'AlignedData'
strand | Class 'AlignedData'
strand-method | Class 'AlignedData'
strand<- | Class 'AlignedData'
strand<--method | Class 'AlignedData'

## -- U --

UniformDispatch | Multiread scoring uniform dispatch

## -- W --

weight | Class 'AlignedData'
weight-method | Class 'AlignedData'
weight<- | Class 'AlignedData'
weight<--method | Class 'AlignedData'
WigRepeatAnalyzer | WIG Repeat Analyzer
writeWIG | Read and Write genomic WIG (fixed step) files

## -- misc --

.testFunctional | Functions dedicated to the functional validation of Pasha package.
.testFunctionalMultiread | Functions dedicated to the functional validation of multiread feature of Pasha package.
.testFunctionalMultiread_generateResults | Functions dedicated to the functional validation of multiread feature of Pasha package.
.testFunctional_generateResults | Functions dedicated to the functional validation of Pasha package.
[-method | Class 'AlignedData'