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Enrichment_FisherTest

Enrichment_FisherTest.Rd

This function performs the Fisher test. The specified variant is

Usage

Enrichment_FisherTest(
  se = NULL,
  variant = NULL,
  use_nocall = FALSE,
  both_as_alt = TRUE,
  trait = NULL,
  trait_levels = NULL
)

Arguments

se

SummarizedExperiment object.

variant

The variant to be analysed. The values for this variant are retrieved from the consensus assay.

use_nocall

Should the NoCall values be used? Then the non genotyped cells would be a separate group in addition to Alt and Ref. If FALSE, the NoCalls are removed. Default = FALSE

both_as_alt

Should the consensus value for heterozyguous (3 or both) be treated as homozyguous (Alt)? Default = TRUE

trait

The trait the variant should be associated to. This can be any column from the colData of the object.

trait_levels

Should only trait levels be used for the comparison? For example, if Sample 1-3 are present but only 1 and 2 should be used in the comparison use trait_levels = c("Sample_1", "Sample_2"). NULL uses all levels. Default = NULL