## Not run:
# #######################################
# ### From the output of the ###
# ### acconpaning python scripts ###
# #######################################
#
# inDir = system.file("extdata", package="pasilla", mustWork=TRUE)
# flattenedfile = file.path(inDir, "Dmel.BDGP5.25.62.DEXSeq.chr.gff")
# sampleData = data.frame(
# condition = c( rep("treated", 3), rep("untreated", 4) ),
# type = c("single", "paired", "paired", "single", "single", "paired", "paired") )
#
# countFiles <- list.files(inDir, pattern="fb.txt")
# rownames( sampleData ) <- countFiles
#
# DEXSeqDataSetFromHTSeq(
# countfiles=file.path( inDir, countFiles ),
# sampleData = sampleData,
# design = ~ sample + exon + type:exon + condition:exon,
# flattenedfile=flattenedfile )
#
#
# #######################################
# ### From GRanges derived objects ###
# #######################################
#
# library(GenomicRanges)
# library(GenomicFeatures)
# library(GenomicAlignments)
#
# hse <- makeTxDbFromBiomart( biomart="ensembl",
# dataset="hsapiens_gene_ensembl" )
#
# bamDir <- system.file(
# "extdata", package="parathyroidSE", mustWork=TRUE )
# fls <- list.files( bamDir, pattern="bam$", full=TRUE )
#
# bamlst <- BamFileList(
# fls, index=character(),
# yieldSize=100000, obeyQname=TRUE )
#
# exonicParts <- disjointExons( hse, aggregateGenes=FALSE )
#
# SE <- summarizeOverlaps( exonicParts, bamlst,
# mode="Union", singleEnd=FALSE,
# ignore.strand=TRUE, inter.feature=FALSE, fragments=TRUE )
#
# colData(SE)$condition <- c("A", "A", "B")
#
# DEXSeqDataSetFromSE( SE,
# design= ~ sample + exon + condition:exon )
#
#
#
# #######################################
# ### From elementary data structures ###
# #######################################
# countData <- matrix( rpois(10000, 100), nrow=1000 )
# sampleData <- data.frame(
# condition=rep( c("untreated", "treated"), each=5 ) )
# design <- formula( ~ sample + exon + condition:exon )
# groupID <- rep(
# paste0("gene", 1:10),
# each= 100 )
# featureID <- rep(
# paste0("exon", 1:100),
# times= 10 )
# DEXSeqDataSet( countData, sampleData, design,
# featureID, groupID )
#
# ## End(Not run)
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