Calculate normalisation factors — rs_calc_norm_factors • bixverse

edgeR's calcNormFactors, via the edge-rs crate.

Usage

rs_calc_norm_factors(counts, lib_size, norm_method)

Arguments

counts: Integer or double matrix. Raw counts of genes x samples.
lib_size: Numeric vector or NULL. Library size per sample. Pass the pre-filter column sums after filtering genes, as edgeR keeps them. NULL uses the column sums of counts.
norm_method: String. One of c("TMM", "TMMwsp", "RLE", "upperquartile", "none"), case-insensitive.

Value

Numeric vector of normalisation factors, one per sample.

References

Robinson and Oshlack, Genome Biol, 2010