BaalChIP: BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Version 1.2.0

The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.

Browse man pages Browse package API and functions Browse package files

AuthorInes de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra SR Chilamakuri, Bruce Ponder, Kerstin Meyer, Florian Markowetz
Bioconductor views Bayesian ChIPSeq Sequencing Software
Date of publicationNone
MaintainerInes de Santiago <inesdesantiago@gmail.com>
LicenseArtistic-2.0
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BaalChIP")

Man pages

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

Functions

BaalChIP Man page Source code
BaalChIP.checks Source code
BaalChIP.get Man page
BaalChIP.get,BaalChIP-method Man page
BaalChIP.report Man page
BaalChIP.report,BaalChIP-method Man page
BaalChIP.run Man page
BaalChIP.run,BaalChIP-method Man page
BaalObject Man page
Bayesian_report Source code
ENCODEexample Man page
FAIREexample Man page
QCfilter Man page
QCfilter,BaalChIP-method Man page
Sum_read_counts Source code
UniqueMappability50bp_hg19 Man page
addVarTable Source code
adjustmentBaalPlot Man page
adjustmentBaalPlot,BaalChIP-method Man page
alleleCounts Man page
alleleCounts,BaalChIP-method Man page
applyAlleleCountsPerBam Source code
applyBayes Source code
applyFilter1allele Source code
applyFilteringStats Source code
applyFiltersPerBam Source code
applyIntBiasFilterPerBam Source code
applyMergeResults Source code
applyReadlenPerBam Source code
applySim Source code
bed2ranges Source code
blacklist_hg19 Man page
checkFileExists Source code
checkmatchingnames Source code
checkmatchingnames.gDNA Source code
createtempdir Source code
estimateRefBias Source code
filter1allele Man page
filter1allele,BaalChIP-method Man page
filterIntbias Man page
filterIntbias,BaalChIP-method Man page
filter_1allele Source code
filter_genomicRegions Source code
filter_intbias Source code
filter_regions Source code
filter_sigi Source code
getASB Man page
getASB,BaalChIP-method Man page
getBaalSlot Source code
getMergedRepData Source code
getRAFfromgDNA Source code
getReport Source code
get_Vartable Source code
get_allele_counts Source code
get_average_stats Source code
get_filterstats Source code
get_lastset Source code
get_mergedcounts Source code
get_readlen Source code
get_simcounts Source code
get_snp_ranges Source code
get_snps_in_GI Source code
getbiasTable Source code
getbiasparam Source code
getdframe Source code
makeARGSTRING Source code
mergePerGroup Man page
mergePerGroup,BaalChIP-method Man page
pickrell2011cov1_hg19 Man page
plot.filt.barplot Source code
plot.filt.boxplot Source code
plot.filt.pie Source code
plot.simul Source code
plotQC Man page
plotQC,BaalChIP-method Man page
plotSimul Man page
plotSimul,BaalChIP-method Man page
plotadjustment Source code
plotfilters Source code
pooldata Source code
readbams Source code
readhettables Source code
readsamplesheet Source code
renameSeqlevels.allowNAs Source code
runBayes Source code
run_sim Source code
summaryASB Man page
summaryASB,BaalChIP-method Man page
summaryQC Man page
summaryQC,BaalChIP-method Man page
summary_ASB Source code
summary_QC Source code
tablenucs Source code
trycreatedir Source code
useRAFfromgDNA Source code
useRAFfromhets Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/BaalChIP-checks.R
R/BaalChIP-class.R
R/BaalChIP-generics.R
R/BaalChIP-methods.R
R/Bayes_report.R
R/QCIntBias.R
R/QCmerged.R
R/QCperBam.R
R/allASBbias.R
R/alleleCounts.R
R/allplots.R
R/allsummary.R
R/applyBayes.R
README.md
build
build/vignette.rds
data
data/ENCODEexample.RData
data/FAIREexample.RData
data/UniqueMappability50bp_hg19.RData
data/baalObject.RData
data/blacklist_hg19.RData
data/datalist
data/pickrell2011cov1_hg19.RData
inst
inst/doc
inst/doc/BaalChIP.R
inst/doc/BaalChIP.Rmd
inst/doc/BaalChIP.html
inst/extra
inst/extra/get.overlaps.v2_chrXY.perl
inst/extra/run_simulations.sh
inst/test
inst/test/AMOVC_hetSNP.txt
inst/test/GM12891_hetSNP.txt
inst/test/MCF7_hetSNP.txt
inst/test/TaT1_hetSNP.txt
inst/test/bamFiles
inst/test/bamFiles/AMOVC_1.test.bam
inst/test/bamFiles/AMOVC_1.test.bam.bai
inst/test/bamFiles/AMOVC_1_gDNA.test.bam
inst/test/bamFiles/AMOVC_1_gDNA.test.bam.bai
inst/test/bamFiles/AMOVC_2.test.bam
inst/test/bamFiles/AMOVC_2.test.bam.bai
inst/test/bamFiles/AMOVC_2_gDNA.test.bam
inst/test/bamFiles/AMOVC_2_gDNA.test.bam.bai
inst/test/bamFiles/GM12891_PAX5_Rep1.bam
inst/test/bamFiles/GM12891_PAX5_Rep1.bam.bai
inst/test/bamFiles/GM12891_PAX5_Rep2.bam
inst/test/bamFiles/GM12891_PAX5_Rep2.bam.bai
inst/test/bamFiles/GM12891_POL2_Rep1.bam
inst/test/bamFiles/GM12891_POL2_Rep1.bam.bai
inst/test/bamFiles/GM12891_POL2_Rep2.bam
inst/test/bamFiles/GM12891_POL2_Rep2.bam.bai
inst/test/bamFiles/GM12891_PU1_Rep1.bam
inst/test/bamFiles/GM12891_PU1_Rep1.bam.bai
inst/test/bamFiles/GM12891_PU1_Rep2.bam
inst/test/bamFiles/GM12891_PU1_Rep2.bam.bai
inst/test/bamFiles/GM12891_TAF1_Rep1.bam
inst/test/bamFiles/GM12891_TAF1_Rep1.bam.bai
inst/test/bamFiles/GM12891_TAF1_Rep2.bam
inst/test/bamFiles/GM12891_TAF1_Rep2.bam.bai
inst/test/bamFiles/MCF7_POL2_Rep1.bam
inst/test/bamFiles/MCF7_POL2_Rep1.bam.bai
inst/test/bamFiles/MCF7_POL2_Rep2.bam
inst/test/bamFiles/MCF7_POL2_Rep2.bam.bai
inst/test/bamFiles/MCF7_STAT3_Rep1.bam
inst/test/bamFiles/MCF7_STAT3_Rep1.bam.bai
inst/test/bamFiles/MCF7_STAT3_Rep2.bam
inst/test/bamFiles/MCF7_STAT3_Rep2.bam.bai
inst/test/bamFiles/MCF7_cFOS_Rep1.bam
inst/test/bamFiles/MCF7_cFOS_Rep1.bam.bai
inst/test/bamFiles/MCF7_cFOS_Rep2.bam
inst/test/bamFiles/MCF7_cFOS_Rep2.bam.bai
inst/test/bamFiles/MCF7_cMYC_Rep1.bam
inst/test/bamFiles/MCF7_cMYC_Rep1.bam.bai
inst/test/bamFiles/MCF7_cMYC_Rep2.bam
inst/test/bamFiles/MCF7_cMYC_Rep2.bam.bai
inst/test/bamFiles/TaT1_1.test.bam
inst/test/bamFiles/TaT1_1.test.bam.bai
inst/test/bamFiles/TaT1_1_gDNA.test.bam
inst/test/bamFiles/TaT1_1_gDNA.test.bam.bai
inst/test/bamFiles/TaT1_2.test.bam
inst/test/bamFiles/TaT1_2.test.bam.bai
inst/test/bamFiles/TaT1_2_gDNA.test.bam
inst/test/bamFiles/TaT1_2_gDNA.test.bam.bai
inst/test/bedFiles
inst/test/bedFiles/AMOVC_peaks_example.bed
inst/test/bedFiles/GM12891_PAX5.bed
inst/test/bedFiles/GM12891_POL2.bed
inst/test/bedFiles/GM12891_POU2F2.bed
inst/test/bedFiles/GM12891_PU1.bed
inst/test/bedFiles/GM12891_TAF1.bed
inst/test/bedFiles/GM12891_YY1.bed
inst/test/bedFiles/MCF7_POL2.bed
inst/test/bedFiles/MCF7_STAT3.bed
inst/test/bedFiles/MCF7_cFOS.bed
inst/test/bedFiles/MCF7_cMYC.bed
inst/test/bedFiles/TaT1_peaks_example.bed
inst/test/exampleChIP.tsv
inst/test/exampleChIP1.tsv
inst/test/exampleChIP2.tsv
inst/test/simuloutput
inst/test/simuloutput/c67c6ec6c433_aln32.bam
inst/test/simuloutput/c67c6ec6c433_aln32.bam.bai
inst/test/simuloutput/c67c6ec6c433_aln32.fasta
inst/test/simuloutput/c67c6ec6c433_aln32.fasta.sam
inst/test/simuloutput/c67c6ec6c433_aln32_snplist.txt
inst/test/simuloutput/c67c6ec6c433_aln34.bam
inst/test/simuloutput/c67c6ec6c433_aln34.bam.bai
inst/test/simuloutput/c67c6ec6c433_aln34.fasta
inst/test/simuloutput/c67c6ec6c433_aln34.fasta.sam
inst/test/simuloutput/c67c6ec6c433_aln36.bam
inst/test/simuloutput/c67c6ec6c433_aln36.bam.bai
inst/test/simuloutput/c67c6ec6c433_aln36.fasta
inst/test/simuloutput/c67c6ec6c433_aln36.fasta.sam
inst/test/simuloutput/c67c6ec6c433_snplist.txt
inst/unitTests
inst/unitTests/test_get_allele_counts.R
man
man/BaalChIP.Rd
man/BaalChIP.get.Rd
man/BaalChIP.report.Rd
man/BaalChIP.run.Rd
man/BaalObject.Rd
man/ENCODEexample.Rd
man/FAIREexample.Rd
man/QCfilter.Rd
man/UniqueMappability50bp_hg19.Rd
man/adjustmentBaalPlot.Rd
man/alleleCounts.Rd
man/blacklist_hg19.Rd
man/filter1allele.Rd
man/filterIntbias.Rd
man/getASB.Rd
man/mergePerGroup.Rd
man/pickrell2011cov1_hg19.Rd
man/plotQC.Rd
man/plotSimul.Rd
man/summaryASB.Rd
man/summaryQC.Rd
tests
tests/runTests.R
vignettes
vignettes/BaalChIP-vignette.bib
vignettes/BaalChIP.Rmd
vignettes/baal.png
vignettes/biomed-central.csl
BaalChIP documentation built on May 20, 2017, 10:04 p.m.