QCfilter: Method QCfilter

In InesdeSantiago/BaalChIP: BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Description

Quality control step for removing variants that may be problematic for identification of allele-specific events.

Usage

QCfilter(.Object, RegionsToFilter = NULL, RegionsToKeep = NULL, verbose = TRUE)

## S4 method for signature 'BaalChIP'
QCfilter(.Object, RegionsToFilter = NULL, RegionsToKeep = NULL, verbose = TRUE)

Arguments

.Object	An object of the BaalChIP class.
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

Value

An updated BaalChIP object with the slot alleleCounts containing a list of GRanges objects that pass filters.

Author(s)

Ines de Santiago

See Also

BaalChIP.get, plotQC, summaryQC

Examples

samplesheet <- system.file("test", "exampleChIP.tsv", package = "BaalChIP")  
hets <- c("MCF7"= system.file("test", "MCF7_hetSNP.txt", package = "BaalChIP"), 
         "GM12891"= system.file("test", "GM12891_hetSNP.txt", package = "BaalChIP"))
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)

InesdeSantiago/BaalChIP documentation built on March 4, 2021, 12:54 a.m.