MARVEL (version 1.4.0)

adhocGene.TabulateExpression.PSI.10x: Dotplot of splice junction expression values for a specified gene

Description

Creates a dotplot of splice junction expression value of a specified gene across different cell groups. The gene and cell groups were defined earlier in adhocGene.TabulateExpression.Gene.10x function.

Usage

adhocGene.TabulateExpression.PSI.10x(MarvelObject, min.pct.cells = 10)

Value

An object of class S3 with new slots MarvelObject$adhocGene$Expression$PSI$Table and MarvelObject$adhocGene$Expression$PSI$Plot.

Arguments

MarvelObject

Marvel object. S3 object generated from adhocGene.TabulateExpression.Gene.10x function.

min.pct.cells

Numeric value. Percentage of cell expressing the splice junction in a cell group, below which, the value be re-coded as missing and appear will be omitted from the plot. A splice junction is considered to be expressed in a given cell if it has count >=1.

Examples

marvel.demo.10x <- readRDS(system.file("extdata/data",
                               "marvel.demo.10x.rds",
                               package="MARVEL")
                               )

# SJ usage profiling
marvel.demo.10x <- adhocGene.TabulateExpression.PSI.10x(
                        MarvelObject=marvel.demo.10x,
                        min.pct.cells=10
                        )

# Check output
marvel.demo.10x$adhocGene$Expression$PSI$Plot