## ----------------------------------------------------------------------------- #library(GenomicRanges) #library(rtracklayer) #library(SummarizedExperiment) #library(Biostrings) #library(Rsamtools) ext.data <- system.file("extdata", package = "miRmine") list.files(ext.data) ## ----------------------------------------------------------------------------- library("miRmine") data(miRmine) miRmine ## ----------------------------------------------------------------------------- adenocarcinoma = miRmine[ , miRmine$Disease %in% c("Adenocarcinoma")] adenocarcinoma as.character(adenocarcinoma$Sample.Accession) ## ----------------------------------------------------------------------------- top.mirna = names(sort(rowSums(assays(adenocarcinoma)$counts))[1]) rowRanges(adenocarcinoma)$mirna_seq[[top.mirna]] ## ----------------------------------------------------------------------------- library("DESeq2") mirmine.subset = miRmine[, miRmine$Tissue %in% c("Lung", "Saliva")] mirmine.subset = SummarizedExperiment( assays = SimpleList(counts=ceiling(assays(mirmine.subset)$counts)), colData=colData(mirmine.subset), rowRanges=rowRanges(mirmine.subset), rowData=NULL ) ddsSE <- DESeqDataSet(mirmine.subset, design = ~ Tissue) ddsSE <- ddsSE[ rowSums(counts(ddsSE)) > 1, ] dds <- DESeq(ddsSE) res <- results(dds) res ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()