getASB: Method getASB

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

Description

getASB identifies allele-specific binding events using a bayesian framework.

Usage

getASB(
  .Object,
  Iter = 5000,
  conf_level = 0.95,
  cores = 4,
  RMcorrection = TRUE,
  RAFcorrection = TRUE,
  verbose = TRUE
)

## S4 method for signature 'BaalChIP'
getASB(
  .Object,
  Iter = 5000,
  conf_level = 0.95,
  cores = 4,
  RMcorrection = TRUE,
  RAFcorrection = TRUE,
  verbose = TRUE
)

Arguments

.Object	An object of the BaalChIP class.
Iter	Maximum number of iterations (default 5000).
conf_level	Confidence interval in the estimated allelic ratio (default 0.95).
cores	number of cores for parallel computing (default is 4).
RMcorrection	Logical value indicating if reference mapping (RM) bias should be applied (default TRUE). If FALSE will not correct for reference allele mapping bias. If TRUE will estimate the RM bias from the overall reference allele proportion.
RAFcorrection	Logical value indicating if relative allele frequency (RAF) bias correction should be applied (default TRUE). If TRUE will read RAF values for each variant from hets files (RAF column name). If FALSE will not correct for relative allele frequency bias.
verbose	logical. If TRUE reports extra information on the process

Value

An updated BaalChIP object with the slot ASB containing variants identified as allele-specific.

Author(s)

Wei Liu, Ke Yuan, Ines de Santiago

See Also

summaryASB, BaalChIP.report

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)
res <- mergePerGroup(res)
res <- getASB(res, cores=2)

#summary - number of significant ASB variants
summaryASB(res)

#report result
res <- BaalChIP.report(res)

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