freq: Summary statistics for genes in an experiment

In RGLab/MAST: Model-based Analysis of Single Cell Transcriptomics

Summary statistics for genes in an experiment

Description

freq returns the frequency of expression, i.e., the proportion of non-zero values in sc. NAs can be optionally removed

Usage

freq(sc, na.rm = TRUE)

condmean(sc)

condSd(sc)

numexp(sc)

Arguments

sc	SingleCellAssay
na.rm	should NAs be removed, or carried through?

Value

vector of proportions

Functions

• condmean(): Report the mean non-zero expression value for each gene. NAs are always removed.

• condSd(): Report standard deviation of expression, for positive et for each gene. NAs are always removed.

• numexp(): Report number of expressing cells ($>0$) per gene. NAs are removed.

Examples

data(vbetaFA)
freq(vbetaFA)
condmean(vbetaFA)

RGLab/MAST documentation built on Sept. 30, 2023, 1:08 p.m.