QCfilter {BaalChIP} | R Documentation |
Method QCfilter
Quality control step for removing variants that may be problematic for identification of allele-specific events.
QCfilter(.Object, RegionsToFilter = NULL, RegionsToKeep = NULL, verbose = TRUE) ## S4 method for signature 'BaalChIP' QCfilter(.Object, RegionsToFilter = NULL, RegionsToKeep = NULL, verbose = TRUE)
.Object |
An object of the |
RegionsToFilter |
a named list of GRanges objects. Variants overlapping these regions will be removed. |
RegionsToKeep |
a named list of GRanges objects. Works in an oposite way to 'RegionstoFilter', variants NOT overlapping these regions will be removed. |
verbose |
logical. If TRUE reports extra information on the process |
An updated BaalChIP
object with the slot alleleCounts
containing a list of GRanges objects that pass filters.
Ines de Santiago
BaalChIP.get
, plotQC
, summaryQC
setwd(system.file('test',package='BaalChIP')) samplesheet <- 'exampleChIP.tsv' hets <- c('MCF7'='MCF7_hetSNP.txt', 'GM12891'='GM12891_hetSNP.txt') res <- BaalChIP(samplesheet=samplesheet, hets=hets) res <- alleleCounts(res, min_base_quality=10, min_mapq=15) data('blacklist_hg19') data('pickrell2011cov1_hg19') data('UniqueMappability50bp_hg19') res <- QCfilter(res, RegionsToFilter=list('blacklist'=blacklist_hg19, 'highcoverage'=pickrell2011cov1_hg19), RegionsToKeep=list('UniqueMappability'=UniqueMappability50bp_hg19)) #check results plotQC(res,'barplot') summaryQC(res)