### R code from vignette source 'blimaTestingData.rnw' ################################################### ### code chunk number 1: style-Sweave ################################################### BiocStyle::latex() ################################################### ### code chunk number 2: blimaTestingData.rnw:22-24 ################################################### library(blimaTestingData) data(blimatesting) ################################################### ### code chunk number 3: blimaTestingData.rnw:28-53 ################################################### library(beadarray) processAllData <- function(dir, useImages=FALSE, illuminaAnnotation=NULL, phenoData, platformName, platformAnnotationPath, processOnly = NULL) { if(missing(dir) | missing(useImages) | missing(illuminaAnnotation) | missing(phenoData) | missing(platformName) | missing(platformAnnotationPath)) { stop("Provide all data!") } x <- readIllumina(dir, useImages, illuminaAnnotation, sectionNames=processOnly); x@experimentData$phenoData <- phenoData; x <- insertSectionData(x, what="Platform", data=rep(platformName, nrow(x@sectionData$numBeads))) x <- addChipsAnnotation(x, platformAnnotationPath); return(x); } addChipsAnnotation <- function(x, platformAnnotationPath) { chipsannotation <- read.AnnotatedDataFrame(platformAnnotationPath); x <- insertSectionData(x, what="Chips", data=pData(chipsannotation)) return(x); } ################################################### ### code chunk number 4: blimaTestingData.rnw:58-80 ################################################### inputDirectory = "/tmp/BLIMATESTINGRAW" outputDirectory = "/tmp" if(file.exists(inputDirectory)) { useImages = TRUE; phenox <- read.AnnotatedDataFrame(file.path(inputDirectory, "annotation_6898481097.csv")); phenoy <- read.AnnotatedDataFrame(file.path(inputDirectory, "annotation_6898481102.csv")); px <- pData(phenox) py <- pData(phenoy) px <- px[px$Name %in% c("A1", "A2", "A3", "A4"),] py <- py[py$Name %in% c("D4", "E1", "E2", "E3", "E4"),] phenox <- AnnotatedDataFrame(data=px) phenoy <- AnnotatedDataFrame(data=py) spotsToReadx <- rownames(px) spotsToReady <- rownames(py) x15 <- processAllData(file.path(inputDirectory,"6898481097"), useImages, "Humanv4", phenox, "HumanHT-12.v4", file.path(inputDirectory, "chips.txt"), processOnly=spotsToReadx) y15 <- processAllData(file.path(inputDirectory, "6898481102"), useImages, "Humanv4", phenoy, "HumanHT-12.v4", file.path(inputDirectory, "chips.txt"), processOnly=spotsToReady) blimatesting <- c(x15, y15) save(blimatesting, file=file.path(outputDirectory, "blimatesting.rda"), compress="xz") } ################################################### ### code chunk number 5: blimaTestingData.rnw:83-111 ################################################### if(file.exists(inputDirectory)) { annotationHumanHT12V4file <-file.path(inputDirectory, "Illumina/annotation/HumanHT-12_V4_0_R2_15002873_B.txt") annotationLines <- readLines(annotationHumanHT12V4file) sections <- grep("^\\[.*\\]$",annotationLines) sections <- c(sections, length(annotationLines) + 1) annotationHumanHT12V4 <- list() for(i in 1:(length(sections)-1)) { row <- sections[i] sectionName <- substr(annotationLines[row], 2, nchar(annotationLines[row])-1) if(sectionName == "Heading") { section <- read.csv(annotationHumanHT12V4file, sep="\t", skip=row, nrows = sections[i+1] - sections[i] - 1, header=FALSE) }else { section <- read.csv(annotationHumanHT12V4file, sep="\t", skip=row, nrows = sections[i+1] - sections[i] - 1) } annotationHumanHT12V4[[length(annotationHumanHT12V4) + 1]] = section names(annotationHumanHT12V4)[i] <- sectionName } save(annotationHumanHT12V4, file=file.path(outputDirectory, "annotationHumanHT12V4.rda"), compress="xz") } ################################################### ### code chunk number 6: blimaTestingData.rnw:114-119 ################################################### if(file.exists(inputDirectory)) { load(file=file.path(outputDirectory, "blimatesting.rda"), envir=.GlobalEnv) load(file=file.path(outputDirectory, "annotationHumanHT12V4.rda"), envir=.GlobalEnv) } ################################################### ### code chunk number 7: blimaTestingData.rnw:124-125 ################################################### data(blimatesting)