View source: R/Enrichment_Fisher.R
Enrichment_FisherTest | R Documentation |
This function performs the Fisher test. The specified variant is
Enrichment_FisherTest(
se = NULL,
variant = NULL,
use_nocall = FALSE,
both_as_alt = TRUE,
trait = NULL,
trait_levels = NULL
)
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 |
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