Implements the Groupwise Truncated Fisher (GTF) score to aggregate groups of p-values from independent tests into a single p-value per group, using an approach derived from Fisher's method. It is designed as an alternative to Fisher's method, that does not suffer as much from the non uniformity of p-values under the null hypothesis, and is expected to work well as long as there is not an enrichment in very low p-values under the null. The API is designed to integrate with the package dplyr, and optionally the package progressr
devtools::install_github("https://github.com/lsdch/gtfisher")
# optional
install.packages("progressr")Computation of scores is fast, but can take a few minutes on large datasets, and takes longer when the simulated sample size is chosen large (see n parameter in gtf_predict()).
This package implements progress signaling using progressr,
which gives freedom to the user on how progress should be reported.
library(gtfisher)
library(progressr) # optional
# no progress bar
group_pvals = gtf_predict(pvals, group, p)
# with progress bar
handlers("progress") # pick your favorite one
with_progress({
group_pvals = gtf_predict(pvals, group, p)
})