MiniMax_calculateStatistic: Calculate the MiniMax Statistics

In TransBioInfoLab/pathwayMultiomics: Implementinig the MiniMax Statistic for Multi-Omics Pathway Analysis

Description

Given a data frame of pathway-level p-values, calculate the MiniMax statistic (but not the significance level of this statistic).

Usage

MiniMax_calculateStatistic(res_df, orderStat = 2L)

Arguments

res_df	A data frame of p-values. The rows correspond to gene sets / pathways and the columns correspond to a data platform for the disease of interest.
orderStat	How many platforms should show a biological signal for a pathway / gene set to have multi-omic "enrichment"? Defaults to 2. See "Details" for more information.

Details

The MiniMax statistic is defined as the minimum of all pairwise maxima of pathway p-values. This operation is arithmetically equivalent to sorting the p-values and taking the second smallest. In our experience, setting this "order statistic" cutoff to 2 is appropriate for =< 5 data platforms. Biologically, this is equivalent to saying "if this pathway is dysregulated in at least two data types for this disease / condition, it is worthy of additional consideration". In situations where more than 5 data platforms are available for the disease of interest, we recommend increasing the orderStat value to 3.

Value

A vector of the MiniMax statistic values.

Examples

  MiniMax_calculateStatistic(multiOmicsHighSignalResults_df[, -(1:2)])

TransBioInfoLab/pathwayMultiomics documentation built on Dec. 18, 2021, 5:12 p.m.