DarioS

GTF2TranscriptDB <- function(gtf.file, out.file = NULL, verbose = TRUE)
{
    require(rtracklayer)
    require(GenomicRanges)
    require(GenomicFeatures)

    min.info <- c("gene_id", "transcript_id", "exon_number")

    if (verbose) message("Importing ", gtf.file)
    gtf <- import.gff(gtf.file, asRangedData = FALSE)

DarioS

setGeneric("rnaCounts", function(alns, tx.db, ...) {standardGeneric("rnaCounts")})

setMethod("unique", "GRangesList",
    function(x)
{
    gr <- unname(unlist(x))
    values(gr)$gene <- rep(names(x), elementLengths(x))
    gr.df <- as.data.frame(gr)
    gr.df <- gr.df[!duplicated(gr.df), ]
    split(GRanges(gr.df$seqnames, IRanges(gr.df$start, gr.df$end), gr.df$strand),

DarioS

.plotValues <- function(data, plot.columns, y.range, y.lab, plot.type, cols, ord, main,
                        g.symbol, first.plot)
{
    if(plot.type == "line")
    {
        matplot(data[, plot.columns, drop = FALSE], ylim = y.range, type = 'l', lty = 1, lwd = 2,
                ylab = y.lab, col = cols, main = main, xaxt = 'n')
        axis(1, 1:nrow(data), ord)
    } else {
        plot.values <- t(data[, plot.columns, drop = FALSE])

DarioS

isoDiff <- function(counts, what = c("exon", "junction", "intronic"), min.count = 0)
{
    unknown.what <- setdiff(what, c("exon", "junction", "intronic"))
    if(length(unknown.what) > 0)
        stop(paste(unknown.what, collapse = ", "), " are invalid values for 'what'.")

    counts.df <- as.data.frame(counts)
    features.keep <- counts.df[, "type"] %in% what
    counts.df <- counts.df[features.keep, ]
    counts.cols <- metadata(counts)[["counts.cols"]] + 5 # Transform relative to all data frame columns.

DarioS

setGeneric("calcFPKMs", function(counts, ...) {standardGeneric("calcFPKMs")})

setMethod("calcFPKMs", c("GRanges"),
    function(counts, verbose = TRUE)
{
    counts.df <- as.data.frame(counts)
    counts.cols <- metadata(counts)[["counts.cols"]] + 5

    # Only use read counts from the known transcriptome.
    counts.df <- counts.df[counts.df[, "type"] %in% c("exon", "junction"), ]

DarioS

07 Sep 2013 04:17:41 [rdesktop] ERROR Error downloading manifest: Network unreachable; LOGGED FROM: void desktop::UpdateChecker::manifestDownloadError(const QString&) /home/ubuntu/rstudio/src/cpp/desktop/DesktopUpdateChecker.cpp:75
07 Sep 2013 04:29:13 [rdesktop] ERROR Error downloading manifest: Network unreachable; LOGGED FROM: void desktop::UpdateChecker::manifestDownloadError(const QString&) /home/ubuntu/rstudio/src/cpp/desktop/DesktopUpdateChecker.cpp:75
08 Sep 2013 05:04:19 [rdesktop] ERROR Error downloading manifest: Network unreachable; LOGGED FROM: void desktop::UpdateChecker::manifestDownloadError(const QString&) /home/ubuntu/rstudio/src/cpp/desktop/DesktopUpdateChecker.cpp:75
08 Sep 2013 22:05:57 [rdesktop] ERROR Error 5 (org.freedesktop.DBus.Error.NoReply): Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken.; LOGGED FROM: void desktop::synct