merge_p_values: Merge a list or matrix of p-values

Description Usage Arguments Value Methods Examples

View source: R/merge_p.r

Description

Merge a list or matrix of p-values

Usage

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merge_p_values(scores, method = "Fisher")

Arguments

scores

Either a list of p-values or a matrix where each column is a test.

method

Method to merge p-values. See 'methods' section below.

Value

If scores is a vector or list, returns a number. If scores is a matrix, returns a named list of p-values merged by row.

Methods

Two methods are available to merge a list of p-values:

Fisher

Fisher's method (default) assumes that p-values are uniformly distributed and performs a chi-squared test on the statistic sum(-2 log(p)). This method is most appropriate when the columns in scores are independent.

Brown

Brown's method extends Fisher's method by accounting for the covariance in the columns of scores. It is more appropriate when the tests of significance used to create the columns in scores are not necessarily independent. Note that the "Brown" method cannot be used with a single list of p-values. However, in this case Brown's method is identical to Fisher's method and should be used instead.

Examples

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  merge_p_values(c(0.05, 0.09, 0.01))
  merge_p_values(list(a=0.01, b=1, c=0.0015, d=0.025), method='Fisher')
  merge_p_values(matrix(data=c(0.03, 0.061, 0.48, 0.052), nrow = 2), method='Brown')

ActivePathways documentation built on July 10, 2020, 1:12 a.m.