# BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

## Documentation for package ‘BaalChIP’ version 1.14.0

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

## Help Pages

adjustmentBaalPlot | Method adjustmentBaalPlot
adjustmentBaalPlot-method | Method adjustmentBaalPlot
alleleCounts | Method alleleCounts
alleleCounts-method | Method alleleCounts
BaalChIP | BaalChIP-class
BaalChIP.get | Method BaalChIP.get
BaalChIP.get-method | Method BaalChIP.get
BaalChIP.report | Method BaalChIP.report
BaalChIP.report-method | Method BaalChIP.report
BaalChIP.run | Method BaalChIP.run
BaalChIP.run-method | Method BaalChIP.run
BaalObject | BaalObject example dataset
blacklist_hg19 | Blacklisted genomic regions
ENCODEexample | ENCODEexample example dataset
FAIREexample | FAIREexample example dataset
filter1allele | Method filter1allele
filter1allele-method | Method filter1allele
filterIntbias | Method filterIntbias
filterIntbias-method | Method filterIntbias
getASB | Method getASB
getASB-method | Method getASB
mergePerGroup | Method mergePerGroup
mergePerGroup-method | Method mergePerGroup
pickrell2011cov1_hg19 | Genomic regions of collapsed repeats
plotQC | Method plotQC
plotQC-method | Method plotQC
plotSimul | Method plotSimul
plotSimul-method | Method plotSimul
QCfilter | Method QCfilter
QCfilter-method | Method QCfilter
summaryASB | Method summaryASB
summaryASB-method | Method summaryASB
summaryQC | Method summaryQC
summaryQC-method | Method summaryQC
UniqueMappability50bp_hg19 | Genomic regions of unique mappability