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 <- statInfo[, c("rawP", "adjP")] diff --git a/vignettes/articles/Figure1.pdf b/vignettes/articles/Figure1.pdf index 4d943ff..48fb2b3 100644 Binary files a/vignettes/articles/Figure1.pdf and b/vignettes/articles/Figure1.pdf differ 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,