## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", dpi = 100 ) ## ---- warning = FALSE, message = FALSE---------------------------------------- library(maser) library(rtracklayer) # Creating maser object using hypoxia dataset path <- system.file("extdata", file.path("MATS_output"), package = "maser") hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h")) # Remove low coverage events hypoxia_filt <- filterByCoverage(hypoxia, avg_reads = 5) ## ---- warning = FALSE, message = FALSE, echo=FALSE---------------------------- knitr::kable( head(availableFeaturesUniprotKB(), 10) ) ## ---- 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 gene specific splicing events srsf6_events <- geneEvents(hypoxia_filt, "SRSF6") srsf6_events ## ---- warning = FALSE, message = FALSE---------------------------------------- # Map transcripts to splicing events srsf6_mapped <- mapTranscriptsToEvents(srsf6_events, ens_gtf) ## ---- warning = FALSE, message = FALSE, eval=FALSE---------------------------- # head(annotation(srsf6_mapped, "SE")) ## ---- warning = FALSE, message = FALSE, echo=FALSE---------------------------- knitr::kable( head(annotation(srsf6_mapped, "SE")) ) ## ---- warning = FALSE, message = FALSE---------------------------------------- # Annotate splicing events with protein features srsf6_annot <- mapProteinFeaturesToEvents(srsf6_mapped, c("Domain_and_Sites", "Topology"), by="category") ## ---- warning = FALSE, message = FALSE, eval=FALSE---------------------------- # head(annotation(srsf6_annot, "SE")) ## ---- warning = FALSE, message = FALSE, echo=FALSE---------------------------- knitr::kable( head(annotation(srsf6_annot, "SE")) ) ## ---- warning = FALSE, message = FALSE---------------------------------------- # Plot splice event, transcripts and protein features plotUniprotKBFeatures(srsf6_mapped, "SE", event_id = 33209, gtf = ens_gtf, features = c("domain", "chain"), show_transcripts = TRUE) ## ---- warning = FALSE, message = FALSE---------------------------------------- ripk2_events <- geneEvents(hypoxia_filt, "RIPK2") ripk2_mapped <- mapTranscriptsToEvents(ripk2_events, ens_gtf) ripk2_annot <- mapProteinFeaturesToEvents(ripk2_mapped, tracks = c("Domain_and_Sites"), by = "category") ## ---- warning = FALSE, message = FALSE---------------------------------------- plotUniprotKBFeatures(ripk2_annot, type = "SE", event_id = 14319, features = c("domain", "binding", "act-site"), gtf = ens_gtf, zoom = FALSE, show_transcripts = TRUE) ## ---- echo=FALSE-------------------------------------------------------------- sessionInfo()