permZero: permZero

In scDD: Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

Description

Function to generate random permutations of nonzero values.

Usage

permZero(m, size, zmat)

Arguments

m	Number of permuted sets to generate.
size	Number of samples present in the dataset
zmat	Matrix of indicators of whether the original data value is zero or not. Should contain the same number of rows and columns as original data matrix.

Details

Generates random permutations for all genes, where the zeroes are kept fixed (i.e. only permute the nonzero condition labels).

Value

a list of length 'm' (nperms) where each item is a 'ngenes' by 'size' matrix

References

Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, Kendziorski C. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1077-y

scDD documentation built on Nov. 8, 2020, 7:10 p.m.