PlotPctExprCells.SJ.10x {MARVEL}

Plot splice junction expression distribution

Description

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

Usage

PlotPctExprCells.SJ.10x(
  MarvelObject,
  cell.group.g1,
  cell.group.g2,
  min.pct.cells.genes = 10,
  min.pct.cells.sj = 10,
  downsample = FALSE,
  downsample.pct.sj = 10,
  seed = 1
)

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.genes

Numeric value. Minimum percentage of cells in which the gene is expressed for that gene to be included for splice junction expression distribution analysis. Expressed genes defined as genes with non-zero normalised UMI counts. This threshold may be determined from PlotPctExprCells.SJ.10x function.

min.pct.cells.sj

Numeric value. Minimum percentage of cells in which the splice junction is expressed for that splice junction to be included for splice junction expression distribution analysis. Expressed splice junctions defined as splice junctions with raw UMI counts >= 1.

downsample

Logical value. If set to TRUE, the splice junctions will be downsampled so that only a smaller number of splice junctions will be included for expression exploration analysis here. Default value is FALSE.

downsample.pct.sj

Numeric value. If downsample set to TRUE, the minimum percentage of splice junctions to include for expression exploration analysis here.

seed

Numeric value. To ensure the splice junctions downsampled will always be reproducible.

Value

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

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 SJ
marvel.demo.10x <- PlotPctExprCells.SJ.10x(
                    MarvelObject=marvel.demo.10x,
                    cell.group.g1=cell.ids.1,
                    cell.group.g2=cell.ids.2,
                    min.pct.cells.genes=5,
                    min.pct.cells.sj=5,
                    downsample=TRUE,
                    downsample.pct.sj=100
                    )

marvel.demo.10x$pct.cells.expr$SJ$Plot
head(marvel.demo.10x$pct.cells.expr$SJ$Data)