From 77c0a494116c540a2a4062bae076963bc1de0dd0 Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Mon, 23 Sep 2024 14:04:32 -0400 Subject: [PATCH] Update lefser version --- R/new_DA_methods.R | 3 ++- vignettes/articles/Figure1.pdf | Bin 16844 -> 16824 bytes .../articles/HMP_2012_16S_gingival_V35.Rmd | 1 - 3 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/new_DA_methods.R b/R/new_DA_methods.R index f7ea010..0343113 100644 --- 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 <- 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z?+54vMEmD}i-(7g>wjdt{5=0F6G|bL6d@4$A2dHNZ;Fki94ap#8XcXCsw~?70aCBM Aod5s; diff --git a/vignettes/articles/HMP_2012_16S_gingival_V35.Rmd b/vignettes/articles/HMP_2012_16S_gingival_V35.Rmd index fd80987..c3a89b6 100644 --- 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,