Read MQuad output

Read output files from MQuad (https://github.com/single-cell-genetics/MQuad).

Usage

ReadMQuad(dir, cb, verbose = TRUE)

Arguments

dir

Path to directory containing MQuad output files

cb

Path to file containing cell barcodes used to run MQuad

verbose

Display messages

Value

Returns a list containing two sparse matrices of alternate allele depth (AD) and total depth (DP) counts.

The AD matrix contains the counts to the alternate allele for the informative mt variant in each cell.

The DP matrix contains the total number of counts for the informative mt variant in each cell.