Don't use NA FDR items for HMP

benjamin-james · benjamin-james · commit 0c631b2268f2 · 2025-02-10T09:41:50.000-05:00
diff --git a/R/deg.R b/R/deg.R
@@ -561,7 +561,7 @@ deg.deseq2 <- function(se,
     
     
     if ("deg" %in% names(S4Vectors::metadata(se))) {
-        S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1/mean(1/pmax(1e-300, df$pvalue[!is.na(df$pvalue)]))
+        S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1/mean(1/pmax(1e-300, df$pvalue[!is.na(df$DESeq2_FDR)]))
     }
     return(se)
 }

Original file line number	Diff line number	Diff line change
`@@ -561,7 +561,7 @@ deg.deseq2 <- function(se,`
`561`	`561`
`562`	`562`
`563`	`563`	`if ("deg" %in% names(S4Vectors::metadata(se))) {`
`564`		`- S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1/mean(1/pmax(1e-300, df$pvalue[!is.na(df$pvalue)]))`
	`564`	`+ S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1/mean(1/pmax(1e-300, df$pvalue[!is.na(df$DESeq2_FDR)]))`
`565`	`565`	`}`
`566`	`566`	`return(se)`
`567`	`567`	`}`