Clean a Filebacked Big Matrix (FBM) by log-transforming and handling NAs

This function inspects an FBM to determine if log-transformation is needed (based on value range) and whether NA values are present. If the maximum value is >= 100 and log2_transform = TRUE, it applies a log2(x + 1) transformation in-place. If any NA values are detected, they are replaced with 0.

Usage

cleanFBM(fbm, ncores = 1, log2_transform = TRUE)

Arguments

fbm

A bigmemory::FBM or bigstatsr::FBM object.

ncores

Integer; number of cores to use for parallel operations (default 1).

log2_transform

Logical; enable automatic log2(x + 1) transformation when the maximum value is at least 100 (default TRUE). Set to FALSE to skip transformation. Missing values are still replaced with zero.

Value

A list with:

max_value

The maximum value encountered in the FBM (after log transformation if applied).

had_na

Logical indicating whether any NA values were found and filled.

Details

Modifies the FBM in place. Uses bigstatsr::big_apply() to process in parallel-safe chunks.

Examples

fbm <- bigstatsr::FBM(3, 4, init = matrix(
    c(0, 1, 2, NA, 100, 200, 300, 400, 5, 6, 7, 8),
    nrow = 3
))
cleanFBM(fbm, ncores = 1)
#> Applying log2 transformation
#> Filling NAs with 0
#> $max_value
#> [1] 400
#> 
#> $had_na
#> [1] TRUE
#>