MARVEL (version 1.4.0)

PropPTC: Tabulate proportion of transcripts with PTC

Description

Tabulates and plots the proportion of transcripts with PTC for each splicing event type.

Usage

PropPTC(MarvelObject, xlabels.size = 8, show.NovelSJ.NoCDS = TRUE, prop.test)

Value

An object of class S3 with new slots MarvelObject$NMD$PTC.Prop$Table, MarvelObject$NMD$PTC.Prop$Plot, and MarvelObject$NMD$PTC.Prop$Plot.Stats.

Arguments

MarvelObject

Marvel object. S3 object generated from FindPTC function.

xlabels.size

Numeric value. Size of the x-axis tick labels. Default is 8.

show.NovelSJ.NoCDS

Logical value. If set to TRUE transcripts not analysed for premature terminal codon (PTC), e.g. non-protein-coding transcripts are tabulated and plotted.

prop.test

Character string. chisq Chi-squared test used to compare the proportion of transcripts with PTC across the different event splicing type. fisher Fisher test used to compare the proportion of transcripts with PTC across the different splicing event type.

Examples

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

marvel.demo <- PropPTC(MarvelObject=marvel.demo,
                       xlabels.size=8,
                       show.NovelSJ.NoCDS=TRUE,
                       prop.test="fisher"
                       )

# Check outputs
head(marvel.demo$NMD$PTC.Prop$Table)
marvel.demo$NMD$PTC.Prop$Plot
marvel.demo$NMD$PTC.Prop$Plot.Stats