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#' simple helper function to split a *RangesList by the strand of its mt target
#'
#' If presented with a GAlignments/MAlignments, this method will split the
#' element by strand, i.e. + alignments and - alignments. Otherwise the method
#' retrieves ranges/variant calls that overlap genic elements on the heavy and
#' light strands of the mitochondrial genome.
#'
#' @param x a *Ranges[List] or *Alignments[List]
#' @param anno optional feature annotation, will use mtAnno.rCRS if NULL
#'
#' @return elements of x over features on each strand OR x split by strand
#'
#' @examples
#' data(RONKSvariants, package="MTseekerData")
#' byStrand(RONKSvariants)
#'
#' @export
byStrand <- function(x, anno=NULL) {
if (is.null(anno)) {
data(mtAnno.rCRS)
anno <- mtAnno
}
stranded <- split(anno, strand(anno))[c("+", "-")]
names(stranded) <- c("heavy", "light")
if (is(x, "MAlignments") | is(x, "GAlignments")) {
split(x, strand(x))
} else if (is(x, "GRanges") | is(x, "MVRanges")) {
sapply(stranded, function(feats) subsetByOverlaps(x, feats))
} else {
sapply(stranded, function(feats) endoapply(x, subsetByOverlaps, feats))
}
}
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