MARVEL (version 1.4.0)

FindPTC: Find premature terminal codons (PTCs)

Description

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

Usage

FindPTC(MarvelObject, method, pval, delta, custom.tran_ids = NULL)

Value

An object of class S3 with new slot MarvelObject$NMD$Prediction.

Arguments

MarvelObject

Marvel object. S3 object generated from CompareValues.PSI and ParseGTF functions.

method

Character string. The statistical method used for differential splicing analysis.

pval

Numeric value. Adjusted p-value below which the splicing event will be analysed for PTCs.

delta

Numeric value. Positive delta percent spliced-in (PSI) value above which the splicing event will be analysed for PTCs. "Positive" because only an increased in PSI value leads to increased alternative exon inclusion in the transcript.

custom.tran_ids

Vector of character strings. Subset of tran_ids to be brought forward for analysis after filtering based on pval and delta.

Examples

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

marvel.demo <- FindPTC(MarvelObject=marvel.demo,
                       method="ad",
                       pval=0.1,
                       delta=90
                       )