MARVEL (version 1.4.0)

CountEvents: Tabulate the number of expressed splicing events

Description

Tabulates and plots the number of expressed splicing events for each splicing event category for a specified cell group.

Usage

CountEvents(MarvelObject, sample.ids, min.cells, event.group.colors = NULL)

Value

An object of class S3 with new slots MarvelObject$N.Events$Table and MarvelObject$N.Events$Plot.

Arguments

MarvelObject

Marvel object. S3 object generated from TransformExpValues function.

sample.ids

Vector of character strings. Sample IDs that constitute the cell group.

min.cells

Numeric value. Minimum number of cells expressing the splicing event for the event to be included for tabulation. A splicing event is defined as expressed when it has a non-missing PSI value.

event.group.colors

Vector of character strings. Colors for the event groups. If not specified, default ggplot2 colors will be used.

Examples

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

# Define cell group for analysis
df.pheno <- marvel.demo$SplicePheno
sample.ids <- df.pheno[which(df.pheno$cell.type=="iPSC"), "sample.id"]

# Tabulate expressed events
marvel.demo <- CountEvents(MarvelObject=marvel.demo,
                           sample.ids=sample.ids,
                           min.cells=5,
                           event.group.colors=NULL
                           )

# Check outputs
marvel.demo$N.Events$Table
marvel.demo$N.Events$Plot