FindPTC.SE.PosStrand {MARVEL}

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)

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.

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.

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)