fisher_exact {structToolbox}R Documentation

fisher_exact class

Description

Fisher's exact test (FET). Applies FET for all features in a DatasetExperiment.

Usage

fisher_exact(alpha = 0.05, mtc = "fdr", factor_name, factor_pred, ...)

Arguments

alpha

the p-value threshold to declare a result 'significant'

mtc

multiple test correction method

factor_name

the sample_meta column to use

factor_pred

A data.frame, with a factor of predicted group labels to compare with factor_name. Can be a data frame with a factor of predictions for each feature.'

...

additional slots and values passed to struct_class

Value

A struct model with functions for applying fisher exact test.

Examples

# load some data
D=MTBLS79_DatasetExperiment()

# prepare predictions based on NA
pred=as.data.frame(is.na(D$data))
pred=lapply(pred,factor,levels=c(TRUE,FALSE))
pred=as.data.frame(pred)

# apply method
M = fisher_exact(alpha=0.05,mtc='fdr',factor_name='class',factor_pred=pred)
M=model_apply(M,D)


[Package structToolbox version 1.0.1 Index]