overlapExprs {scran} | R Documentation |
Compute the gene-specific overlap in expression profiles between two groups of cells.
## 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)
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 |
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 |
BPPARAM |
A BiocParallelParam object to use in |
... |
Additional arguments to pass to the matrix method. |
assay.type |
A string specifying which assay values to use, e.g., |
get.spikes |
See |
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
.
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 pairwiseWilcox
and combineMarkers
for the component functions.
See findMarkers
for the equivalent function using t-tests.
# 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)