Bugfix test

caravagnalab · Jun 6, 2024 · ac32240 · ac32240
1 parent 9e5eb05
commit ac32240
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/R/test.R b/R/test.R
@@ -56,7 +56,7 @@ test_de <- function(devil.fit, contrast, pval_adjust_method = "BH", max_lfc = 10
       H <- compute_hessian(devil.fit$beta[gene_idx,], 1 / devil.fit$overdispersion[gene_idx], devil.fit$input_matrix[gene_idx,], devil.fit$design_matrix, devil.fit$size_factors)
       total_variance <- t(contrast) %*% H %*% contrast
       #1 - stats::pchisq(mu_test^2 / total_variance, df = 1)
-      2 * stats::pt(abs(mu_test) / sqrt(total_variance), df = ncol(Y) - 2, lower.tail = F)
+      2 * stats::pt(abs(mu_test) / sqrt(total_variance), df = nsamples - 2, lower.tail = F)
     }, mc.cores = n.cores) %>% unlist()
   }