getASB {BaalChIP} | R Documentation |
Method getASB
getASB identifies allele-specific binding events using a bayesian framework.
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)
.Object |
An object of the |
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 |
verbose |
logical. If TRUE reports extra information on the process |
An updated BaalChIP
object with the slot ASB
containing variants identified as allele-specific.
Wei Liu, Ke Yuan, Ines de Santiago
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)