MARVEL (version 1.4.0)

PlotPctExprCells.Genes.10x: Plot gene expression distribution

Description

Generates a plot of gene expression distribution (percentage of cells expressing a particular gene) to determine normalised gene expression threshold for downstream differential splice junction analysis.

Usage

PlotPctExprCells.Genes.10x(
  MarvelObject,
  cell.group.g1,
  cell.group.g2,
  min.pct.cells = 1
)

Value

An object of class S3 with a new slots MarvelObject$pct.cells.expr$Gene$Plot and MarvelObject$pct.cells.expr$Gene$Data.

Arguments

MarvelObject

Marvel object. S3 object generated from CheckAlignment.10x function.

cell.group.g1

Vector of character strings. Cell IDs corresponding to Group 1 (reference group) of downstream differential splice junction analysis.

cell.group.g2

Vector of character strings. Cell IDs corresponding to Group 2 of downstream differential splice junction analysis.

min.pct.cells

Numeric value. Minimum percentage of cells in which the gene is expressed for that gene to be included for gene expression distribution analysis. Expressed genes defined as genes with non-zero normalised UMI counts.

Examples

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

# Define cell groups
    # Retrieve sample metadata
    sample.metadata <- marvel.demo.10x$sample.metadata

    # Group 1 (reference)
    index <- which(sample.metadata$cell.type=="iPSC")
    cell.ids.1 <- sample.metadata[index, "cell.id"]
    length(cell.ids.1)

    # Group 2
    index <- which(sample.metadata$cell.type=="Cardio day 10")
    cell.ids.2 <- sample.metadata[index, "cell.id"]
    length(cell.ids.2)

# Explore % of cells expressing genes
marvel.demo.10x <- PlotPctExprCells.Genes.10x(
                        MarvelObject=marvel.demo.10x,
                        cell.group.g1=cell.ids.1,
                        cell.group.g2=cell.ids.2,
                        min.pct.cells=5
                        )

# Check output
marvel.demo.10x $pct.cells.expr$Gene$Plot
head(marvel.demo.10x $pct.cells.expr$Gene$Data)