Conditionally apply log2 transformation on assay data based on log2_assays parameter.

Usage

cond_log2_transform_assays(
  assay_data,
  log2_assays,
  threshold = 30,
  reverse = FALSE,
  prettify_names = TRUE,
  invert_assays = FALSE
)

Arguments

assay_data: A list containing matrices as assay data.
log2_assays: A string parameter that can be NULL, empty, or a non-empty string. If NULL: log2 transformation will be guessed based on input assays. If empty: no log2 transformation will be applied. If non-empty: log2 transformation will be applied unconditionally to specified assays.
threshold: A numeric threshold to determine if the matrix should be log-transformed. This is only checked if should_transform is NULL.
reverse: Boolean, should we unlog rather than log?
prettify_names: Boolean. Prettify element names? Passed to validate_indices().
invert_assays: Boolean, apply transform to assays NOT specified in log2_assays.

Value

A modified assay_data list.

Examples

assay_data <- list(
  counts = matrix(c(1, 100, 1000, 5, 50, 500), nrow = 3,
    dimnames = list(paste0("gene", 1:3), c("s1", "s2")))
)
cond_log2_transform_assays(assay_data, log2_assays = "1")
#> $counts
#>             s1       s2
#> gene1 0.000000 2.321928
#> gene2 6.643856 5.643856
#> gene3 9.965784 8.965784
#>