census: Applies the Census count transformation on a count matrix

In omnideconv/SimBu: Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Applies the Census count transformation on a count matrix

Description

needs a sparse matrix with cells in columns and genes in rows. You can find the detailed explaination here: http://cole-trapnell-lab.github.io/monocle-release/docs/#census

Usage

census(
  matrix,
  exp_capture_rate = 0.25,
  expr_threshold = 0,
  BPPARAM = BiocParallel::bpparam(),
  run_parallel = FALSE
)

Arguments

matrix	sparse count matrix; cells in columns, genes in rows
exp_capture_rate	expected capture rate; default=0.25
expr_threshold	expression threshold; default=0
BPPARAM	BiocParallel::bpparam() by default; if specific number of threads x want to be used, insert: BiocParallel::MulticoreParam(workers = x)
run_parallel	boolean, decide if multi-threaded calculation will be run. FALSE by default

Value

a vector for each cell-type, with a scaling factor which can be used to transform the counts of the matrix

Examples

tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE)
tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm))
cen <- SimBu::census(tpm)

omnideconv/SimBu documentation built on May 5, 2024, 12:33 p.m.