TPM calculation — calculate_tpm • bixverse

TPM calculation

Usage

calculate_tpm(counts, gene_lengths)

Arguments

counts: Numeric matrix. Count matrix (gene x sample)
gene_lengths: Named vector. Named vector with gene lengths.

Value

TPM-normalised matrix.

Examples

# TPM over synthetic counts with flat 2kb gene lengths
syn <- synthetic_bulk_cor_matrix()
gene_lengths <- stats::setNames(
  rep(2000, nrow(syn$counts)),
  rownames(syn$counts)
)
tpm <- calculate_tpm(syn$counts, gene_lengths)
colSums(tpm)[1:3]
#> sample_1 sample_2 sample_3 
#>    1e+06    1e+06    1e+06