combinePvalues {multiGSEA} | R Documentation |
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.
combinePvalues(df, method = "stouffer", weights = NULL)
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. |
method |
String that specifies the method to combine multiple p-values. Default: "stouffer" Options: "stouffer", "fisher", "edgington" |
weights |
List of weights that will be used in a weighted Stouffer method. |
Vector of length nrow(df)
with combined p-values.
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")