overlapExprs {scran}R Documentation

Overlap expression profiles

Description

Compute the gene-specific overlap in expression profiles between two groups of cells.

Usage

## S4 method for signature 'ANY'
overlapExprs(x, groups, gene.names=rownames(x), block=NULL, 
    pval.type=c("any", "all"), direction=c("any", "up", "down"), tol=1e-8, 
    log.p=FALSE, full.stats=FALSE, subset.row=NULL, BPPARAM=SerialParam()) 

## S4 method for signature 'SingleCellExperiment'
overlapExprs(x, ..., subset.row=NULL, assay.type="logcounts",
    get.spikes=FALSE) 

Arguments

x

A numeric matrix of expression values, where each column corresponds to a cell and each row corresponds to an endogenous gene. Alternatively, a SingleCellExperiment object containing such a matrix.

groups

A vector of group assignments for all cells.

gene.names

A character vector of gene names with one value for each row of x.

block

A factor specifying the blocking level for each cell.

pval.type

A string specifying the type of combined p-value to be computed, i.e., Simes' or IUT.

direction

A string specifying which direction of change in expression should be used to rank genes in the output.

tol

A numeric scalar specifying the tolerance with which ties are considered.

log.p

A logical scalar indicating if log-transformed p-values/FDRs should be returned.

full.stats

A logical scalar indicating whether all statistics (i.e., raw and BH-adjusted p-values) should be returned for each pairwise comparison.

subset.row

See ?"scran-gene-selection".

BPPARAM

A BiocParallelParam object to use in bplapply for parallel processing.

...

Additional arguments to pass to the matrix method.

assay.type

A string specifying which assay values to use, e.g., "counts" or "logcounts".

get.spikes

See ?"scran-gene-selection".

Details

This function provides a convenience wrapper for marker gene identification, based on running pairwiseTTests and passing the result to combineMarkers. All of the arguments above are supplied directly to one of these two functions.

Note that log.p only affects the combined p-values and FDRs. If full.stats=TRUE, the p-values for each pairwise comparison will be log-transformed regardless of the value of log.p.

Value

A named list of DataFrames, each of which contains a sorted marker gene list for the corresponding cluster. See ?combineMarkers for more details on the output format.

See Also

See pairwiseWilcox and combineMarkers for the component functions.

See findMarkers for the equivalent function using t-tests.

Examples

# Using the mocked-up data 'y2' from this example.
example(computeSpikeFactors) 
y2 <- normalize(y2)
groups <- sample(3, ncol(y2), replace=TRUE)
out <- overlapExprs(y2, groups, subset.row=1:10)

[Package scran version 1.10.2 Index]