MARVEL (version 1.4.0)

FindPTC.SE.PosStrand: Find premature terminal codon (PTC) for skipped-exon (SE) located on the positive strand of the transcript

Description

Finds PTC(s) introduced by alternative exons into protein-coding transcripts.

Usage

FindPTC.SE.PosStrand(MarvelObject, tran_id, gene_id)

Value

A data frame of transcripts containing splicing events meeting the psi.de.sig and psi.de.diff criteria are categorised based on the presence or absence of PTCs.

Arguments

MarvelObject

S3 object generated from CompareValues.PSI and ParseGTF function.

tran_id

Character string. Vector of tran_id to look for PTCs.

gene_id

Character string. Vector of gene_id corresponding to the tran_id argument.

Details

This function finds PTC(s) introduced by alternative exons into protein-coding transcripts. It also records the distance between a PTCs and the final splice junction for a given protein-coding transcript. Non-protein-coding transcripts or transcripts in which splicing events are located outside of the transcripts' open-reading frame (ORF) are not analysed for PTCs but are noted.

Examples

marvel.demo <- readRDS(system.file("extdata/data", "marvel.demo.rds", package="MARVEL"))

# Define relevant event type
results <- marvel.demo$DE$PSI$Table[["ad"]]
index.1 <- which(results$event_type=="SE")
index.2 <- grep(":+@", results$tran_id, fixed=TRUE)
index <- intersect(index.1, index.2)
results <- results[index, ]
tran_id <- results$tran_id[1]
gene_id <- results$gene_id[1]

# Find PTC
results <- FindPTC.SE.PosStrand(MarvelObject=marvel.demo,
                                tran_id=NULL,
                                gene_id=gene_id
                                )

# Check output
head(results)