VariantSelection_VMR: VariantSelection_VMR

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

VariantSelection_VMR

Description

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?

CostaLab/sigurd documentation built on Feb. 10, 2025, 11:08 p.m.