VariantSelection_VMR — VariantSelection_VMR • sigurd

This is an adaption of the VMR based selection of variants from Miller et al. This selection process is designed for ATAC data and not scRNAseq data.

Usage

VariantSelection_VMR(
  SE,
  stabilize_variance = TRUE,
  low_coverage_threshold = 10,
  minimum_fw_rev_reads = 2,
  verbose = TRUE
)

Arguments

SE: SummarizedExperiment object.
stabilize_variance: Should the variance be stabilized by using the mean allele frequency for cells with a low coverage? Coverage threshold is set by low_coverage_threshold.
low_coverage_threshold: Cells below this threshold are set to the mean.
minimum_fw_rev_reads: How many forward and reverse reads should a cell have? Default = 2
verbose: Should the function be verbose?