Github repository for adaptively weighted fisher's method (AW-Fisher)
library(devtools)
install_github("Caleb-Huo/AWFisher")
Huo, Z., Tang, S., Park, Y. and Tseng, G., 2020. P-value evaluation, variability index and biomarker categorization for adaptively weighted Fisher’s meta-analysis method in omics applications. Bioinformatics, 36(2), pp.524-532.
The manuscript can be found here: https://www.ncbi.nlm.nih.gov/pubmed/31359040
library(AWFisher)
K <- 50 ## combining K studies
G <- 10000 ## simulate G genes
set.seed(15213)
p.values = matrix(runif(K*G), ncol=K) ## This should be a matrix (if not, try as.matrix) instead of a dataframe.
res = AWFisher_pvalue(p.values)
hist(res$pvalues, breaks=40)
ks<-ks.test(res$pvalues, "punif", min=0, max=1, alternative = "two.sided"); ## KS test to test if the AW p-values are uniformly distributed under the null
ks
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