VariantSelection_VMR_Group: VariantSelection_VMR_Group

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

VariantSelection_VMR_Group

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. The variants are first selected as described. Then the average allele frequency between the the two groups of interest are compared. If the allele frequency in group1 is higher than the required threshold, the variant is retained.

Usage

VariantSelection_VMR_Group(
  SE,
  stabilize_variance = TRUE,
  low_coverage_threshold = 10,
  minimum_fw_rev_reads = 2,
  group_of_interest = NULL,
  group1 = NULL,
  group2 = NULL,
  group_factor = 5,
  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
group_of_interest	The group of interest in the column data.
group1	The group of interest.
group2	The second group.
group_factor	How much higher should the VAF be in group 1 comapred to group 2? Default = 5
verbose	Should the function be verbose?

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