Count bam files on interval to create count indexes

Source: R/preprocessing_filtering_reduction.R

Count bam files on interval to create count indexes

bams_to_matrix_indexes(dir, which, BPPARAM = BiocParallel::bpparam())

Arguments

dir

A directory containing single cell BAM files and BAI files
which

Genomic Range on which to count
BPPARAM

BPPARAM object for multiprocessing. See bpparam for more informations. Will take the default BPPARAM set in your R session.

Value

A list containing a "feature index" data.frame and a count vector for non 0 entries, both used to form the sparse matrix