calcExprFreqs: calcExprFreqs
In muscat: Multi-sample multi-group scRNA-seq data analysis tools

Description Usage Arguments Details Value Author(s) Examples

Calculates gene expression frequencies

1	calcExprFreqs(x, assay = "counts", th = 0)

`x`	a `SingleCellExperiment`.
`assay`	a character string specifying which assay to use.
`th`	numeric threshold value above which a gene should be considered to be expressed.

calcExprFreq computes, for each sample and group (in each cluster), the fraction of cells that express a given gene. Here, a gene is considered to be expressed when the specified measurement value (assay) lies above the specified threshold value (th).

a SingleCellExperiment containing, for each cluster, an assay of dimensions #genes x #samples giving the fraction of cells that express each gene in each sample. If colData(x) contains a "group_id" column, the fraction of expressing cells in each each group will be included as well.

Helena L Crowell & Mark D Robinson

data(sce)
library(SingleCellExperiment)

frq <- calcExprFreqs(sce)

# one assay per cluster
assayNames(frq)  

# expression frequencies by
# sample & group; 1st cluster:
head(assay(frq))