Update lefser version

waldronlab · Sep 23, 2024 · 77c0a49 · 77c0a49
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commit 77c0a49
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Showing 3 changed files with 2 additions and 2 deletions.
diff --git a/R/new_DA_methods.R b/R/new_DA_methods.R
@@ -262,7 +262,8 @@ DA_lefse <- function(
     statInfo$rawP <- seq(0.04, 0, length.out = nrow(statInfo))
     statInfo$adjP <- seq(0.09, 0, length.out = nrow(statInfo))
     # statInfo$adj_pval <- stats::p.adjust(statInfo$rawP, method = "fdr")
-    rownames(statInfo) <- statInfo[["features"]] ## check names
+    rownames(statInfo) <- statInfo[["features"]] ## lefser version 1.15
+    rownames(statInfo) <- statInfo[["Names"]] ## lefser version 1.14
     colnames(statInfo) <- c("Taxa", "LDA_scores", "abs_score", "rawP", "adjP")
 
     pValMat <- statInfo[, c("rawP", "adjP")]

diff --git a/vignettes/articles/Figure1.pdf b/vignettes/articles/Figure1.pdf
diff --git a/vignettes/articles/HMP_2012_16S_gingival_V35.Rmd b/vignettes/articles/HMP_2012_16S_gingival_V35.Rmd
@@ -242,7 +242,6 @@ enrichment <- createEnrichment(
     priorKnowledge = prior_info,
     enrichmentCol = "taxon_annotation",
     namesCol = "new_names",
-    # slot = "pValMat", colName = "adjP", type = "pvalue",
     slot = slotV, colName = colNameV, type = typeV,
     direction = direction,
     threshold_pvalue = adjThr,