Another check:
My hg18.fa constructed from hg18 UCSC from TopHat website has the size of 3131776827 bytes, same as yours?
My hg18.fa constructed from hg18 UCSC from TopHat website has the size of 3131776827 bytes, same as yours?
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mapResultBatch1 <- c("group1_file1", "group1_file2") mapResultBatch2 <- c("group2_file2", "group2_file2") outputDir <- "DEGseq_out_dir" refFlat <- "gene annotation in refFlat format" DEGseq(mapResultBatch1, mapResultBatch2, fileFormat="bed", refFlat=refFlat, outputDir=outputDir, method="MARS")
# get gene express mapResultBatch <- c("group1_file1", "group1_file2", "group2_file2", "group2_file2") output <- "gene.exp" refFlat <- "gene annotation in refFlat format" exp <- getGeneExp(mapResultBatch, refFlat = refFlat, output = output) # apply samWrapper geneExpFile <- "gene.exp" set.seed(100) geneExpFile1 <- geneExpFile geneExpFile2 <- geneExpFile output <- "samWrapperOut.txt" expCol1 = c(2, 4) expCol2 = c(6, 8) measure1 = c(-1, -2) measure2 = c(1, 2) samWrapper(geneExpFile1 = geneExpFile1, geneCol1 = 1, expCol1 = expCol1, measure1 = measure1, geneExpFile2 = geneExpFile2, geneCol2 = 1, expCol2 = expCol2, measure2 = measure2, nperms = 100, min.foldchange = 2, max.qValue = 1e-04, output = output, paired = TRUE)
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