Column-ranks an expression matrix. If stable_genes is provided, uses the
stable-genes ranking method (unit-normalised ranks against a small set of
stable genes); otherwise standard column ranks. Sets attr(., "stable") so
downstream singscore functions know which bounds formula to use.
Usage
calc_singscore_rank(exp, stable_genes = NULL)
Arguments
- exp
Numerical matrix. Rows = genes, columns = samples.
- stable_genes
Character vector or NULL. Gene names of stable genes.
Defaults to NULL (standard ranking).
Value
A rank matrix with the same shape as exp and attr(., "stable")
set to TRUE or FALSE.
References
1.) Foroutan et al., BMC Bioinformatics, 2018.; 2.) Bhuva,
et al., Nucleic Acids Res., 2020
Examples
# column ranks of an expression matrix, ready for singscore
set.seed(123L)
exp_mat <- matrix(
rnorm(200 * 10),
nrow = 200,
dimnames = list(sprintf("gene_%03i", 1:200), sprintf("sample_%i", 1:10))
)
ranks <- calc_singscore_rank(exp_mat)
dim(ranks)
#> [1] 200 10
