convertCellScoresToCounts: Convert abundance measurements to cell counts

In SpatialDecon: Deconvolution of mixed cells from spatial and/or bulk gene expression data

Description

Converts cell abundance scores to cell counts, under the assumption that the observation with the greatest sum of cell abundance scores is 100

Usage

convertCellScoresToCounts(beta, nuclei.counts = NULL, omit.tumor = FALSE)

Arguments

beta	Matrix of cell abundance scores, with cells in rows and observations in columns. The assumption is that this matrix is from well-normalized data.
nuclei.counts	Optional. A vector of total nuclei counts. If provided, the function will output not only cells.per.100 but also total cells.
omit.tumor	Logical. If FALSE, any rows of beta with "tumor" in their name will be omitted.

Value

A list with two elements, each a rescaled version of beta. cells.per.100 gives estimated percents of total, and cell.counts is cells.per.100 * nuclei.counts.

SpatialDecon documentation built on Nov. 8, 2020, 6 p.m.