spelling error

benjamin-james · benjamin-james · commit 4cafa5d23a59 · 2025-09-29T10:13:34.000-04:00
diff --git a/R/deg.R b/R/deg.R
@@ -571,7 +571,7 @@ deg.deseq2 <- function(se,
         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)$deg[[paste0(prefix, "_adj_harmonic_mean_pvalue")]] <- min(1, sum(1/seq(length(pvalue))) / mean(1./pval, na.rm=TRUE))
+        S4Vectors::metadata(se)$deg[[paste0(prefix, "_adj_harmonic_mean_pvalue")]] <- min(1, sum(1/seq(length(pval))) / mean(1./pval, na.rm=TRUE))
     }
     return(se)
 }

Original file line number	Diff line number	Diff line change
`@@ -571,7 +571,7 @@ deg.deseq2 <- function(se,`
`571`	`571`	`pval[pval < 1e-300] <- 1e-300`
`572`	`572`	`pval[is.na(df$padj)] <- NA`
`573`	`573`	`S4Vectors::metadata(se)$deg[[paste0(prefix, "_harmonic_mean_pvalue")]] <- 1./mean(1./pval, na.rm=TRUE)`
`574`		`- S4Vectors::metadata(se)$deg[[paste0(prefix, "_adj_harmonic_mean_pvalue")]] <- min(1, sum(1/seq(length(pvalue))) / mean(1./pval, na.rm=TRUE))`
	`574`	`+ S4Vectors::metadata(se)$deg[[paste0(prefix, "_adj_harmonic_mean_pvalue")]] <- min(1, sum(1/seq(length(pval))) / mean(1./pval, na.rm=TRUE))`
`575`	`575`	`}`
`576`	`576`	`return(se)`
`577`	`577`	`}`