## ----setup, echo=FALSE, results="hide"---------------------------------------- library(BiocStyle) knitr::opts_chunk$set(tidy=FALSE, cache=FALSE, dev="png", message=FALSE, error=FALSE, warning=TRUE) ## ----package-select,message=FALSE--------------------------------------------- library(isomiRs) data(mirData) head(isoSelect(mirData, mirna="hsa-let-7a-5p", 1000)) ## ----package-load,message=FALSE----------------------------------------------- library(isomiRs) data(mirData) ## ----package-plot-iso,message=FALSE,eval=FALSE-------------------------------- # ids <- IsomirDataSeqFromFiles(fn_list, design=de) ## ----package-plot-iso-t5,message=FALSE---------------------------------------- ids <- isoCounts(mirData) isoPlot(ids, type="all") ## ----package-count,message=FALSE---------------------------------------------- head(counts(ids)) ## ----package-norm,message=FALSE----------------------------------------------- library(pheatmap) ids = isoNorm(ids, formula = ~ condition) pheatmap(counts(ids, norm=TRUE)[1:100,], annotation_col = data.frame(colData(ids)[,1,drop=FALSE]), show_rownames = FALSE, scale="row") ## ----package-isoannotation---------------------------------------------------- head(isoAnnotate(ids)) ## ----package-de,message=FALSE------------------------------------------------- dds <- isoDE(ids, formula=~condition) library(DESeq2) plotMA(dds) head(results(dds, format="DataFrame")) ## ----package-de-iso5,message=FALSE-------------------------------------------- dds = isoDE(ids, formula=~condition, ref=TRUE, iso5=TRUE) head(results(dds, tidy=TRUE)) ## ----package-de-with-deseq2--------------------------------------------------- dds = DESeqDataSetFromMatrix(counts(ids), colData(ids), design = ~condition) ## ----isonetwork, message=FALSE, error=FALSE, fig.height=12, fig.width=7------- # library(org.Mm.eg.db) # library(clusterProfiler) data(isoExample) # ego <- enrichGO(row.names(assay(gene_ex_rse, "norm")), # org.Mm.eg.db, "ENSEMBL", ont = "BP") data = isoNetwork(mirna_ex_rse, gene_ex_rse, target = ma_ex, enrich = ego, summarize = "group") isoPlotNet(data, minGenes = 4) ## ----findtarget--------------------------------------------------------------- mirna_ma <- data.frame(gene = names(gene_ex_rse)[1:20], mir = names(mirna_ex_rse)) ma_ex <- findTargets(mirna_ex_rse, gene_ex_rse, mirna_ma) head(ma_ex[,1:4]) ## ----mirna2targetscan--------------------------------------------------------- library(targetscan.Hs.eg.db) mirna_ma <- mirna2targetscan(c("hsa-miR-34c-5p")) head(mirna_ma) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()