VariantCloneSizeThresholding

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