lianos

setMethod("order", "GenomicRanges",
    function(..., ignore.strand=FALSE, na.last=TRUE, decreasing=FALSE) {
        if (!isTRUEorFALSE(decreasing)) {
            stop("'decreasing' must be TRUE or FALSE")
        }
        args <- list(...)
        if (length(args) != 1L) {
            stop("ordering more than one GRanges is undefined")
        }
        x <- args[[1L]]

lianos

#!/bin/bash

## This script was originally written by Kasper Daniel Hansen on a post to bioc-devel
## in order to illustrate how you can have two versions of R running at the same time
## on OS X:
##
## https://stat.ethz.ch/pipermail/bioc-devel/2011-July/002684.html
##
## This is posted without any guarantees that it will work, and will obviously have
## to be changed to different degrees as new versions of R come out.

lianos

library(Biostrings)

setGeneric("rho", function(x, ...) standardGeneric("rho"))

setMethod("rho", c(x="XStringSet"),
function(x, ...) {
  if (!xsbasetype(x) %in% c("DNA", "RNA")) {
    stop("`x` must be of DNA or RNA base type")
  }
  di <- oligonucleotideFrequency(x, 2L, as.prob=TRUE)

lianos

library(seqc)

##' Creates an ExpressionSet of counts for a given subset of the samples
##' provided by the seqc data package.
##'
##' Currently this only works for \code{feature == 'gene'}.
##'
##' @param feature The type of features you want to build an ExpressionSet
##'   out of (gene, junction, taqman
##' @param annotation If \code{feature == 'gene'}, then this determines which