Read MGATK output

Read output files from MGATK (https://github.com/caleblareau/mgatk).

ReadMGATK(dir, verbose = TRUE)

Arguments

dir

Path to directory containing MGATK output files

verbose

Display messages

Value

Returns a list containing a sparse matrix (counts) and two dataframes (depth and refallele).

The sparse matrix contains read counts for each base at each position and strand.

The depth dataframe contains the total depth for each cell. The refallele dataframe contains the reference genome allele at each position.

Examples

if (FALSE) {
data.dir <- system.file("extdata", "test_mgatk", package="Signac")
mgatk <- ReadMGATK(dir = data.dir)
}