aggregatePvals {HTSanalyzeR} | R Documentation

## Aggregate p-values from gene set over-representation tests.

### Description

This function takes as input a matrix of p-values for example obtained from a GSEA on multiple phenotypes, with a row for each gene set and a column for each phenotype and aggregates the p-values by row (i.e. one aggregated p-value for each gene set) according to Fisher or Stouffer's methods.

### Usage

    aggregatePvals(pvalMatrix, method="fishers", pAdjustMethod="BH",
    order=TRUE)

### Arguments

`pvalMatrix` | a numeric matrix of p-values, with rows named according to the gene set (rows correspond to gene sets, and columns to multiple p-values to be aggregated for that gene set)
`method` | a single character value of "stouffers" or "fishers"
`pAdjustMethod` | a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details)
`order` | a single logical value: TRUE or FALSE. If it is TRUE, the results table will be ordered according to the aggregated p-values.

### Details

The Fisher method combines the p-values into an aggregated chi-squared statistic equal to -2*sum(log(Pk)) were we have k=1,..,K pvalues independently distributed as uniform on the unit interval under the null hypothesis. The resulting p-values are calculated by comparing this chi-squared statistic to a chi-squared distribution with 2K degrees of freedom. The Stouffer method computes a z-statistics assuming that the sum of the quantiles (from a standard normal distribution) corresponding to the p-values are distributed as N(0,K).

### Value

a matrix with a row for each gene set and two columns: "Aggregated.p.value" and "Adjusted.aggregated.p.value"

### Author(s)

Jack Rose and Camille Terfve

### Examples

    p1 <- runif(100, min=0, max=1)
    p2 <- runif(100, min=0, max=1)
    names(p1) <- as.character(sample(x=seq(from=1, to=100, by=1), size=100,
    replace=FALSE))
    pmatrix <- cbind(p1, p2)
    rownames(pmatrix) <- names(p1)
    aggP <- aggregatePvals(pvalMatrix=pmatrix, method="stouffers")

[Package HTSanalyzeR version 2.36.0 Index]