Normalize a single-cell count matrix

Counts are expected with features in rows and cells in columns.

Usage

cuda_normalize_counts(counts, scale_factor = 10000, log1p = TRUE)

Arguments

counts

A base matrix, Matrix sparse matrix, or cudasparse.

scale_factor

Target library size.

log1p

Whether to apply log1p() to non-zero normalized values.

Value

A sparse Matrix::dgCMatrix with the input feature and cell names.

Examples

counts <- Matrix::Matrix(matrix(c(1, 0, 3, 2, 4, 1), 3), sparse = TRUE)
cuda_normalize_counts(counts)
#> 3 x 2 sparse Matrix of class "dgCMatrix"
#>                       
#> [1,] 7.824446 7.957927
#> [2,] .        8.650900
#> [3,] 8.922792 7.265130