seByArm: seByArm: split a SummarizedExperiment by chromosomal arm

In ttriche/regulatoR: robust detection of regulatoRy associations between loci and features

Usage

seByArm(SE, GRorGRL = NULL, build = "hg19")

Arguments

SE
GRorGRL
build

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (SE, GRorGRL = NULL, build = "hg19") 
{
    stopifnot(is(SE, "SummarizedExperiment"))
    if (!is.null(GRorGRL)) {
        stopifnot(unique(genome(GRorGRL)) == build)
        stopifnot(class(GRorGRL) %in% c("GRanges", "GRangesList"))
        stopifnot(unique(genome(rowData(SE))) == unique(genome(GRorGRL)))
    }
    else {
        data(hg19.by.arm)
        GRorGRL <- hg19.by.arm
    }
    if (is(GRorGRL, "GRanges")) 
        GRL <- split(GRorGRL)
    else GRL <- GRorGRL
    lapply(GRL, function(x) SE[names(subsetByOverlaps(rowData(SE), 
        x)), ])
  }

ttriche/regulatoR documentation built on June 1, 2019, 2:51 a.m.