Calculate Tsallis diversity per gene across samples

Calculate Tsallis diversity per gene across samples

Usage

calculate_diversity(
  x,
  genes = NULL,
  norm = TRUE,
  tpm = FALSE,
  assayno = 1,
  verbose = FALSE,
  q = 2,
  what = c("S", "D"),
  nthreads = 1
)

Arguments

x

A numeric matrix or data.frame of transcript-level expression values (rows = transcripts, columns = samples), or a SummarizedExperiment- like object.

genes

Character vector assigning each transcript (row) to a gene. Must have length equal to nrow(x) or the number of transcripts in `x`.

norm

Logical; if TRUE, normalize Tsallis entropy to [0,1] per gene.

tpm

Logical. If TRUE and `x` is a tximport-style list, use the `$abundance` matrix instead of `$counts`.

assayno

Integer assay index to use when `x` is a SummarizedExperiment.

verbose

Logical; print diagnostic messages when TRUE.

q

Numeric scalar or vector of Tsallis q values to evaluate (q > 0). If length(q) > 1, the result will contain separate columns per sample and q.

what

Which quantity to return: 'S' for Tsallis entropy or 'D' for Hill numbers.

nthreads

Number of threads for parallel processing (default: 1). Set to > 1 to parallelize per-gene entropy calculations.

Value

A SummarizedExperiment with assay `diversity` containing per-gene diversity values.

Examples

data('tcga_brca_luma', package = 'TSENAT')
rc <- as.matrix(tcga_brca_luma[1:20, -1, drop = FALSE])
gs <- tcga_brca_luma[1:20, 1]
se <- calculate_diversity(rc, gs, q = 0.1, norm = TRUE)
SummarizedExperiment::assay(se)[1:3, 1:3]
#>      TCGA-A7-A0CH_N TCGA-A7-A0CH_T TCGA-A7-A0D9_N
#> NA               NA             NA             NA
#> NA.1             NA             NA             NA
#> NA.2             NA             NA             NA