NBumiCoexpression {M3Drop} | R Documentation |
Ranks genes by residual dispersion from mean-dispersion power-law relationship.
NBumiCoexpression(counts, fit, gene_list=NULL, method=c("both", "on", "off"))
counts |
raw count matrix (e.g. from NBumiConvertData). |
fit |
output from NBumiFitModel or NBumiFitBasicModel. |
gene_list |
set of gene names to test coexpression of. |
method |
type of coexpression to test (see: Details). |
Tests for co-expression using the normal approximation of a binomial test. Co-expression is defined according to the method argument as follows:
two genes are both >0 in more cells than expected.
two genes are both 0 in more cells than expected.
two genes are either both >0 or both 0 in more cells than expected.
In all cases the null expectation is calculated using the fit library-size adjusted negative binomial model. This remove spurious co-expression due to cells with differing numbers of detected genes.
a matrix of Z-scores for each pair of genes in the provided gene list.
library(M3DExampleData) counts <- NBumiConvertData(Mmus_example_list$data) fit <- NBumiFitModel(counts); genes <- c("Sox2", "Eomes", "Zscan4d", "Obox1", "Obox3") co <- NBumiCoexpression(counts, fit, genes, method="both"); on <- NBumiCoexpression(counts, fit, genes, method="on"); off <- NBumiCoexpression(counts, fit, genes, method="off");