From 238805f01be739b1283b9cc4ab50a7f02aa6e92b Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Thu, 12 Sep 2024 13:55:12 -0400 Subject: [PATCH] Change column for plotting positives and negatives from adjP to rawP --- vignettes/articles/HMP_2012_16S_gingival_V13.Rmd | 2 +- vignettes/articles/Ravel_2011_16S_BV.Rmd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/vignettes/articles/HMP_2012_16S_gingival_V13.Rmd b/vignettes/articles/HMP_2012_16S_gingival_V13.Rmd index c3dd8a1..ac169d0 100644 --- a/vignettes/articles/HMP_2012_16S_gingival_V13.Rmd +++ b/vignettes/articles/HMP_2012_16S_gingival_V13.Rmd @@ -241,7 +241,7 @@ positives <- createPositives( object = DA_output, priorKnowledge = prior_info, enrichmentCol = "taxon_annotation", namesCol = "new_names", - slot = "pValMat", colName = "adjP", type = "pvalue", + slot = "pValMat", colName = "rawP", type = "pvalue", # direction = direction, direction = direction, threshold_pvalue = 1, diff --git a/vignettes/articles/Ravel_2011_16S_BV.Rmd b/vignettes/articles/Ravel_2011_16S_BV.Rmd index 5bd9f54..c5022f8 100644 --- a/vignettes/articles/Ravel_2011_16S_BV.Rmd +++ b/vignettes/articles/Ravel_2011_16S_BV.Rmd @@ -218,7 +218,7 @@ positives <- createPositives( object = DA_output, priorKnowledge = prior_info, enrichmentCol = "taxon_annotation", namesCol = "taxon_name", - slot = "pValMat", colName = "adjP", type = "pvalue", + slot = "pValMat", colName = "rawP", type = "pvalue", direction = direction, threshold_pvalue = 1, threshold_logfc = 0,