getTestsModTable: Extract table of phenotypic variable tests from 'K2' object

In montilab/K2Taxonomer: Creating annotated submodules of high-throughput data through recursive partitioning

Extract table of phenotypic variable tests from 'K2' object

Description

Create table phenotypic variable results from 'K2' object.

Usage

getTestsModTable(K2res)

Arguments

K2res

An object of class K2 or K2results().

Value

A data.frame object with the following columns:

• value: The variable being tested

• node: The partition label

• edge: The subgroup for the given partition

• pval: Nominal p-value of test

• fdr: Benjamini-Hochberg FDR corrected p-value

• df: Degrees of freedom of test

• stat: Test statistic

• obsMean: Mean value across partition members

• altMean: Mean value for all other observations

• diffMean: Difference is mean

• nhits: The number of second label values in subgroup

• ncase: The total second-level label value

• nalt: The total first-level label value

• ndrawn: The total members in the subgroup

• hits: Members of subgroup with second-level label value

• test: The statistical test that produced this result

References

\insertRef

reed_2020K2Taxonomer \insertRefbhK2Taxonomer

Examples

## Read in ExpressionSet object
library(Biobase)
data(sample.ExpressionSet)

## Pre-process and create K2 object
K2res <- K2preproc(sample.ExpressionSet)

## Run K2 Taxonomer algorithm
K2res <- K2tax(K2res,
            stabThresh=0.5)

infoClassVector <- c(sex='factor', score='numeric1')

K2res <- runTestsMods(K2res, infoClass=infoClassVector)

head(getTestsModTable(K2res))

montilab/K2Taxonomer documentation built on Jan. 25, 2024, 4:29 p.m.