Merge branch 'dev' of https://github.com/kellislab/benj into dev

benjamin-james · benjamin-james · commit d0f53725f02d · 2025-03-10T14:10:41.000-04:00
diff --git a/R/deg.R b/R/deg.R
@@ -565,8 +565,7 @@ deg.deseq2 <- function(se,
         pval <- df$pvalue
         pval[pval < 1e-300] <- 1e-300
         pval[is.na(df$padj)] <- NA
-        S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1./mean(1./pval, na.rm=TRUE)
-    }
+        S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1./mean(1./pval, na.rm    }
     return(se)
 }
 

Original file line number	Diff line number	Diff line change
`@@ -565,8 +565,7 @@ deg.deseq2 <- function(se,`
`565`	`565`	`pval <- df$pvalue`
`566`	`566`	`pval[pval < 1e-300] <- 1e-300`
`567`	`567`	`pval[is.na(df$padj)] <- NA`
`568`		`- S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1./mean(1./pval, na.rm=TRUE)`
`569`		`- }`
	`568`	`+ S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1./mean(1./pval, na.rm }`
`570`	`569`	`return(se)`
`571`	`570`	`}`
`572`	`571`