Scale deconvoluted cell fractions to cell densities

Scale deconvoluted cell fractions to cell densities

get_densities(DCres, density_info)

Arguments

DCres

Data.frame of deconvoluted cell fractions computed with the run_quantiseq() function, with sample identifiers as row names.

density_info

Named numeric vector of total cell densities per sample. The vector names should match the sample identifiers specified in DCres. These values are derived from the quantitative analysis of imaging data.

Value

A data.frame of cell densities, samples by cell types.

Examples

data(dataset_racle)
mixture <- dataset_racle$expr_mat

res_quantiseq_run <- quantiseqr::run_quantiseq(
  expression_data = dataset_racle$expr_mat,
  signature_matrix = "TIL10",
  is_arraydata = FALSE,
  is_tumordata = TRUE,
  scale_mRNA = TRUE
)
#> 
#> Running quanTIseq deconvolution module
#> Gene expression normalization and re-annotation (arrays: FALSE)
#> Removing 17 noisy genes
#> Removing 15 genes with high expression in tumors
#> Signature genes found in data set: 135/138 (97.83%)
#> Mixture deconvolution (method: lsei)
#> Deconvolution successful!

totcells <- rnorm(n = ncol(mixture), mean = 1e4)
names(totcells) <- colnames(mixture)
celldens <- get_densities(res_quantiseq_run, totcells)