Mercurial > repos > shians > shrnaseq
diff hairpinTool.R @ 8:548802b3492f
Version 1.0.9
- Added R session info to output
- Added email for bug reports
- Changed edgeR requirement to be stopping condition
- Changed names of gene-wise comparison tables to "gene_level" from "roast"
- Fixed selection of multiple genes for barcode plotting
author | shian_su <registertonysu@gmail.com> |
---|---|
date | Fri, 02 May 2014 17:22:24 +1000 |
parents | 91e411fcdecc |
children | f1076bfb0ed1 |
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--- a/hairpinTool.R Wed Apr 23 14:05:26 2014 +1000 +++ b/hairpinTool.R Fri May 02 17:22:24 2014 +1000 @@ -58,7 +58,11 @@ library(limma, quietly=TRUE, warn.conflicts=FALSE) if (packageVersion("edgeR") < "3.5.23") { - message("Please update 'edgeR' to version >= 3.5.23 to run this script") + stop("Please update 'edgeR' to version >= 3.5.23 to run this tool") +} + +if (packageVersion("limma")<"3.19.19") { + message("Update 'limma' to version >= 3.19.19 to see updated barcode graphs") } ################################################################################ @@ -305,12 +309,13 @@ smearPng[i] <- makeOut(paste0("smear(", contrastData[i], ").png")) smearPdf[i] <- makeOut(paste0("smear(", contrastData[i], ").pdf")) topOut[i] <- makeOut(paste0("toptag(", contrastData[i], ").tsv")) - roastOut[i] <- makeOut(paste0("roast(", contrastData[i], ").tsv")) + roastOut[i] <- makeOut(paste0("gene_level(", contrastData[i], ").tsv")) barcodePng[i] <- makeOut(paste0("barcode(", contrastData[i], ").png")) barcodePdf[i] <- makeOut(paste0("barcode(", contrastData[i], ").pdf")) } } countsOut <- makeOut("counts.tsv") +sessionOut <- makeOut("session_info.txt") # Initialise data for html links and images, table with the link label and # link address @@ -346,7 +351,7 @@ selectVals <- as.numeric(unique(selectVals)) } else { selectVals <- gsub(" ", "", selectVals, fixed=TRUE) - selectVals <- unlist(strsplit(selectVals, " ")) + selectVals <- unlist(strsplit(selectVals, ",")) } } @@ -593,7 +598,7 @@ write.table(roastData, file=roastOut[i], row.names=FALSE, sep="\t") linkName <- paste0("Gene Level Analysis Table(", contrastData[i], ") (.tsv)") - linkAddr <- paste0("roast(", contrastData[i], ").tsv") + linkAddr <- paste0("gene_level(", contrastData[i], ").tsv") linkData <- rbind(linkData, c(linkName, linkAddr)) if (selectOpt=="rank") { selectedGenes <- rownames(roastData)[selectVals] @@ -636,6 +641,7 @@ } } +# Generate data frame of the significant differences sigDiff <- data.frame(Up=upCount, Flat=flatCount, Down=downCount) if (workMode == "glm") { row.names(sigDiff) <- contrastData @@ -643,13 +649,19 @@ row.names(sigDiff) <- paste0(pairData[2], "-", pairData[1]) } +# Output table of summarised counts ID <- rownames(data$counts) outputCounts <- cbind(ID, data$counts) -write.table(outputCounts, file=countsOut, row.names=FALSE, sep="\t") +write.table(outputCounts, file=countsOut, row.names=FALSE, sep="\t", + quote=FALSE) linkName <- "Counts table (.tsv)" linkAddr <- "counts.tsv" linkData <- rbind(linkData, c(linkName, linkAddr)) +# Record session info +writeLines(capture.output(sessionInfo()), sessionOut) +linkData <- rbind(linkData, c("Session Info", "session_info.txt")) + # Record ending time and calculate total run time timeEnd <- as.character(Sys.time()) timeTaken <- capture.output(round(difftime(timeEnd,timeStart), digits=3)) @@ -730,7 +742,7 @@ cata("<h4>Plots:</h4>\n") for (i in 1:nrow(linkData)) { - if (!grepl(".tsv", linkData$Link[i])) { + if (grepl(".pdf", linkData$Link[i])) { HtmlLink(linkData$Link[i], linkData$Label[i]) } } @@ -756,7 +768,7 @@ } if (cpmReq!=0 && sampleReq!=0) { - tempStr <- paste("Hairpins with less than", cpmReq, + tempStr <- paste("Hairpins without more than", cpmReq, "CPM in at least", sampleReq, "samples are insignificant", "and filtered out.") ListItem(tempStr) @@ -807,6 +819,14 @@ ListItem(cit[4]) cata("</ol>\n") +cata("<p>Report problems to: su.s@wehi.edu.au</p>\n") + +for (i in 1:nrow(linkData)) { + if (grepl("session_info", linkData$Link[i])) { + HtmlLink(linkData$Link[i], linkData$Label[i]) + } +} + cata("<table border=\"0\">\n") cata("<tr>\n") TableItem("Task started at:"); TableItem(timeStart)