mergePerGroup: Method mergePerGroup

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

Description

Merges all ChIP-seq datasets within a group of samples creating a data.frame that contains allele-specific read count data for all variants that need to be analysed.

Usage

mergePerGroup(.Object)

## S4 method for signature 'BaalChIP'
mergePerGroup(.Object)

Arguments

.Object

An object of the BaalChIP class.

Details

if QCfilter has been applied, will use the most up-to-date variant set available for each individual BAM file (after QC). Missing values are allowed for heterozygous variants that are not available (e.g. do not pass filter for a particular ChIP-seq dataset).

Value

An updated BaalChIP object with the slot mergedCounts containing a data.frame of merged samples per group.

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))

res <- mergePerGroup(res)

#retrieve mergedCounts:
counts <- BaalChIP.get(res, 'mergedCounts')

#mergedCounts are grouped by group_name:
names(counts)
sapply(counts, dim)

#check out the result for one of the groups:
head(counts[[1]])

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