## ----setup, include = FALSE------------------------------------------------ knitr::opts_chunk$set( collapse = TRUE, comment = "#>", dpi = 100 ) ## ---- warning = FALSE, message = FALSE------------------------------------- library(maser) library(rtracklayer) # path to Hypoxia data path <- system.file("extdata", file.path("MATS_output"), package = "maser") hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"), ftype = "ReadsOnTargetAndJunctionCounts") ## ---- warning = FALSE, message = FALSE------------------------------------- hypoxia ## ---- warning = FALSE, message = FALSE, eval=FALSE------------------------- # head(summary(hypoxia, type = "SE")[, 1:8]) ## ---- warning = FALSE, message = FALSE, echo=FALSE------------------------- knitr::kable( head(summary(hypoxia, type = "SE")[, 1:8]) ) ## ---- warning = FALSE, message = FALSE------------------------------------- hypoxia_filt <- filterByCoverage(hypoxia, avg_reads = 5) ## ---- warning = FALSE, message = FALSE------------------------------------- hypoxia_top <- topEvents(hypoxia_filt, fdr = 0.05, deltaPSI = 0.1) hypoxia_top ## ---- warning = FALSE, message = FALSE------------------------------------- hypoxia_mib2 <- geneEvents(hypoxia_filt, geneS = "MIB2", fdr = 0.05, deltaPSI = 0.1) print(hypoxia_mib2) ## ---- warning = FALSE, message = FALSE------------------------------------- maser::display(hypoxia_mib2, "SE") ## ---- warning = FALSE, message = FALSE------------------------------------- plotGenePSI(hypoxia_mib2, type = "SE", show_replicates = TRUE) ## ---- warning = FALSE, message = FALSE, fig.small = TRUE------------------- volcano(hypoxia_filt, fdr = 0.05, deltaPSI = 0.1, type = "SE") ## ---- warning = FALSE, message = FALSE, fig.small = TRUE------------------- dotplot(hypoxia_top, type = "SE") ## ---- warning = FALSE, message = FALSE------------------------------------- ## Ensembl GTF annotation gtf_path <- system.file("extdata", file.path("GTF","Ensembl85_examples.gtf.gz"), package = "maser") ens_gtf <- rtracklayer::import.gff(gtf_path) ## ---- warning = FALSE, message = FALSE------------------------------------- ## Retrieve SRSF6 splicing events srsf6_events <- geneEvents(hypoxia_filt, geneS = "SRSF6", fdr = 0.05, deltaPSI = 0.1 ) ## Dislay affected transcripts and PSI levels plotTranscripts(srsf6_events, type = "SE", event_id = 33209, gtf = ens_gtf, zoom = FALSE, show_PSI = TRUE) ## ---- warning = FALSE, message = FALSE------------------------------------- stat2_events <- geneEvents(hypoxia_filt, geneS = "STAT2", fdr = 0.05, deltaPSI = 0.1 ) plotTranscripts(stat2_events, type = "RI", event_id = 3785, gtf = ens_gtf, zoom = FALSE) ## ---- warning = FALSE, message = FALSE------------------------------------- il32_events <- geneEvents(hypoxia_filt, geneS = "IL32", fdr = 0.05, deltaPSI = 0.1 ) plotTranscripts(il32_events, type = "MXE", event_id = 1136, gtf = ens_gtf, zoom = FALSE) ## ---- warning = FALSE, message = FALSE------------------------------------- #A5SS event bcs1l_gene <- geneEvents(hypoxia_filt, geneS = "BCS1L", fdr = 0.05, deltaPSI = 0.1 ) plotTranscripts(bcs1l_gene, type = "A5SS", event_id = 3988, gtf = ens_gtf, zoom = TRUE) ## ---- echo=FALSE----------------------------------------------------------- sessionInfo()