Produce long form quality metrics for each cell-variant pair for read depth, allele frequency, and genotype quality — quality_output • scDNA

Produce long form quality metrics for each cell-variant pair for read depth, allele frequency, and genotype quality

Usage

quality_output(
  file,
  filter = TRUE,
  input_variants,
  input_cells,
  NGT,
  DP_cut = 10,
  AF_cut = 20,
  GQ_cut = 20
)

Arguments

file: path to H5 file
filter: default=TRUE, determines whether function should output filtered or unfiltered long form matrix containing per cell-variant pair of NGT, DP, AF, GQ metrics
input_variants: variants of interest to collect QC data
input_cells: cells of interest to subset on
NGT: NGT matrix
DP_cut: read depth cutoff
AF_cut: allele frequency cutoff
GQ_cut: genotype quality cutoff

Value

filtered NGT matrix containing NAs for cells that do not pass QC