% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/enrichment_functions.R

\name{combinePvalues}

\alias{combinePvalues}

\title{Calculate a combined p-value for multiple omics layer.}

\usage{

combinePvalues(df, method = "stouffer", col_pattern = "pval", weights = NULL)

}

\arguments{

\item{df}{Data frame where rows represent a certain pathway or gene set and

columns represent p-values derived from independent tests, e.g., different

omics layer.}

\item{method}{String that specifies the method to combine multiple p-values.

Default: "stouffer" Options: "stouffer", "fisher", "edgington"}

\item{col_pattern}{String of the pattern that specifies the columns to be

combined. Default: "pval", Options: "pval", "padj" (legacy)}

\item{weights}{List of weights that will be used in a weighted Stouffer

method.}

}

\value{

Vector of length \code{nrow(df)} with combined p-values.

}

\description{

This function applies the Stouffer method, the Edgington method or the

Fisher\'s combined probability test to combine p-values of independent tests

that are based on the same null hypothesis. The Stouffer method can also be

applied in a weighted fashion.

}

\examples{

df <- cbind(runif(5), runif(5), runif(5))

colnames(df) <- c("trans.pval", "prot.pval", "meta.pval")

# run the unweighted summation of z values

combinePvalues(df)

# run the weighted variant

combinePvalues(df, weights = c(10, 5, 1))

# run the Fisher's combined probability test

combinePvalues(df, method = "fisher")

# run the Edgington's method

combinePvalues(df, method = "edgington")

}