getASB: Method getASB

Description Usage Arguments Value Author(s) See Also Examples

Description

Method getASB

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

Usage

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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

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

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

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

Bioconductor-mirror/BaalChIP documentation built on May 29, 2017, 12:04 a.m.