changed p value computation to be in log space, to handle more extreme values (8da49317) · Commits · github_fork / Presto 20250701

R/glmm.R

+8 −2

Original line number	Diff line number	Diff line
		@@ -347,7 +347,8 @@ toptable.presto <- function(
		) %>%
		dplyr::mutate(
		wald = beta / sigma,
		pval = 2 * (1 - pnorm(abs(beta / sigma)))
		pval = -2 * pnorm(abs(beta / sigma), log.p = TRUE)
		# pval = 2 * (1 - pnorm(abs(beta / sigma)))
		) %>%
		dplyr::mutate(fdr = p.adjust(pval, 'BH')) %>%
		subset(pval < max_pval & beta > min_beta & beta < max_beta & fdr < max_fdr)
		@@ -403,7 +404,12 @@ effects.presto <- function(object, effects) {
		suppressMessages({
		object$effect <- dplyr::full_join(beta_tidy, sigma_tidy) %>%
		dplyr::left_join(object$log_mu) %>%
		dplyr::mutate(wald = beta/sigma, pval = 2 * (1 - pnorm(abs(beta/sigma)))) %>%

		dplyr::mutate(
		wald = beta/sigma,
		pval = -2 * pnorm(abs(beta / sigma), log.p = TRUE)
		# pval = 2 * (1 - pnorm(abs(beta/sigma)))
		) %>%
		dplyr::mutate(fdr = p.adjust(pval, "BH"))
		})
		return(object)