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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 |
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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"), ] |
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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. |
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.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]) |
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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), |
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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) |