MARVEL (version 1.4.0)

PropModality.Bar: Modality proportion broken down by event type

Description

Tabulates and plots the proportion of each modality broken down by splicing event type.

Usage

PropModality.Bar(
  MarvelObject,
  modality.column,
  modality.type,
  event.type,
  xlabels.size = 8,
  zoom = FALSE,
  yinterval = NULL,
  prop.test,
  prop.adj
)

Value

An object of class S3 containing new slots MarvelObject$Modality$Prop$BarChart$Table and MarvelObject$Modality$Prop$BarChart$Stats.

Arguments

MarvelObject

Marvel object. S3 object generated from AssignModality function.

modality.column

Character string. Can take the value "modality", "modality.var" or "modality.bimodal.adj". Please refer to AssignModality function help page for more details.

modality.type

Character string. basic indicates that only the main modalities (included, excluded, bimodal, middle, multimodal) are analysed. Sub-modalities (primary and dispersed) will be merged. extended indicates that both main and sub-modalities are analysed. Sub-modalities will not be merged.

event.type

Character string. To indicate which event type to analyse. Can take the value "SE", "MXE", "RI", "A5SS" or "A3SS". Specify "all" to include all event types.

xlabels.size

Numeric value. Size of x-axis labels as per ggplot2 function. Default is 8.

zoom

Logical value. If set to TRUE, users can specify the range of the y-axis using yinterval argument. Useful when scrutinasing low-frequency event types, e.g. middle and multimodal.

yinterval

Logical value. Only applicable when zoom is set to TRUE.

prop.test

Character string. Only applicable when across.event.type set to TRUE. chisq Chi-squared test used to compare the proportion of modalities across the different event splicing type. fisher Fisher test used to compare the proportion of modalities across the different splicing event type.

prop.adj

Character string. Only applicable when across.event.type set to TRUE. Adjust p-values generated from prop.test for multiple testing. Options available as per p.adjust function.

Examples

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

marvel.demo <- PropModality.Bar(MarvelObject=marvel.demo,
                                modality.column="modality.bimodal.adj",
                                modality.type="extended",
                                event.type=c("SE", "MXE", "RI", "A5SS", "A3SS", "AFE", "ALE"),
                                prop.test="fisher",
                                prop.adj="fdr"
                                )

# Check outputs
head(marvel.demo$Modality$Prop$BarChart$Table)
marvel.demo$Modality$Prop$BarChart$Plot
marvel.demo$Modality$Prop$BarChart$Stats