Cross-subject Covariance of Relative Abundance

This function is for calculating the cross-subject covariance of relative abundance for selected cell types.

music_Sigma.ct(x, non.zero, markers, clusters, samples, select.ct)

Arguments

x

SingleCellExperiment, single cell dataset

non.zero

logical, if true, remove all gene with zero expression

markers

vector or list of gene names

clusters

character, the ColData used as clusters

samples

character,the ColData used as samples

select.ct

vector of cell types included, default as NULL. If NULL, include all cell types in x

Value

celltype^2 by gene matrix of covariance