EstimatePCACellTypeProportions {BisqueRNA}

Estimate cell type proportions using first PC of expression matrix

Description

Estimate cell type proportions using first PC of expression matrix

Usage

EstimatePCACellTypeProportions(x, weighted = FALSE, w = NULL)

Arguments

x

A sample by gene bulk expression matrix. Genes should be marker genes

weighted

Boolean. If weighted=TRUE, multiply scaled gene expression by gene weights

w

Numeric vector. Weights of genes

Value

ret List. Attribute pcs contains matrix of PCs, where PC1 should be used as estimates for cell type abundances Attribute sdev contains eigenvalues of eigendecomposition of var-covar matrix. The 1st eigenvalue should explain most of the variance. Attribute genes contains names of genes.