## ----message=FALSE------------------------------------------------------------ library(fastseg) ## ----------------------------------------------------------------------------- data(coriell) head(coriell) samplenames <- colnames(coriell)[4:5] data <- as.matrix(coriell[4:5]) #data[is.na(data)] <- median(data, na.rm=TRUE) chrom <- coriell$Chromosome maploc <- coriell$Position ## ----------------------------------------------------------------------------- library("GenomicRanges") ## with both individuals gr <- GRanges(seqnames=chrom, ranges=IRanges(maploc, end=maploc)) mcols(gr) <- data colnames(mcols(gr)) <- samplenames res <- fastseg(gr) head(res) ## with one individual gr2 <- gr data2 <- as.matrix(data[, 1]) colnames(data2) <- "sample1" mcols(gr2) <- data2 res <- fastseg(gr2) head(res) ## ----message=FALSE------------------------------------------------------------ library(oligo) eSet <- new("ExpressionSet") assayData(eSet) <- list(intensity=data) featureData(eSet) <- new("AnnotatedDataFrame", data=data.frame( chrom = paste("chr",chrom,sep=""), start = maploc, end = maploc,stringsAsFactors=FALSE)) phenoData(eSet) <- new("AnnotatedDataFrame", data=data.frame(samples=samplenames)) sampleNames(eSet) <- samplenames res <- fastseg(eSet) head(res) ## ----------------------------------------------------------------------------- data2 <- data[, 1] res <- fastseg(data2) head(res) ## ----------------------------------------------------------------------------- data2 <- data[1:400, ] res <- fastseg(data2) head(res) ## ----------------------------------------------------------------------------- ## with both individuals gr <- GRanges(seqnames=chrom, ranges=IRanges(maploc, end=maploc)) mcols(gr) <- data colnames(mcols(gr)) <- samplenames res <- fastseg(gr,segMedianT=0.2) ## ----------------------------------------------------------------------------- segPlot(gr,res, plot.type="w") ## ----fig.height=10, fig.width=10, message=FALSE------------------------------- segPlot(gr, res, plot.type="s") ## ----------------------------------------------------------------------------- data(fastsegData) system.time(res <- fastseg(fastsegData)) ## ----------------------------------------------------------------------------- segPlot(fastsegData,res, plot.type="w") ## ----message=FALSE------------------------------------------------------------ library(DNAcopy) cna <- DNAcopy::CNA(fastsegData,chrom="chr1",maploc=1:length(fastsegData)) system.time(res2 <- DNAcopy::segment(cna)) ## ----------------------------------------------------------------------------- plot(res2, plot.type="w", xmaploc=TRUE) ## ----eval=FALSE--------------------------------------------------------------- # toBibtex(citation("fastseg"))