VariantCloneSizeThresholding: VariantCloneSizeThresholding

In CostaLab/sigurd: Single cell Genotyping Using RNA Data

VariantCloneSizeThresholding

Description

We get variants of interest using a clone size thresholding. Source: https://github.com/petervangalen/MAESTER-2021

Usage

VariantCloneSizeThresholding(
  SE,
  min_coverage = 2,
  fraction_negative_cells = 0.9,
  min_clone_size = 10,
  vaf_threshold = 0.5,
  verbose = TRUE
)

Arguments

SE	SummarizedExperiment object.
min_coverage	Minimum coverage a variant needs to have.
fraction_negative_cells	The fraction of negative cells needed.
min_clone_size	minimum number of cells.
vaf_threshold	Variant Allele Threshold. Cells above this threshold are considered mutated.
verbose	Should the function be verbose? Default = TRUE

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