From dd2928e78dae5f2b3f7f2a8caa38f9da5ba871b9 Mon Sep 17 00:00:00 2001 From: Ben Siranosian Date: Wed, 15 Dec 2021 07:21:51 -0800 Subject: [PATCH] Change filtering in ALDEx2 differential abundance to be slightly less stringent. Make it more clear what the filter is applying --- scripts/post_classification_workflow.R | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/scripts/post_classification_workflow.R b/scripts/post_classification_workflow.R index 1a84350..9758587 100644 --- a/scripts/post_classification_workflow.R +++ b/scripts/post_classification_workflow.R @@ -506,8 +506,9 @@ if (nrow(sample.groups) < 3){ # AT A SPECIFIC TAX LEVEL: filtering # keep only those samples with > min.reads min.reads <- 5000 - # keep only OTUs with an abundance of at least 0.01 - min.prop = 0.01 + # keep only OTUs with an FRACTION of at least 0.001 + # This is equivalent to a PERCENTAGE of 0.1 + min.prop = 0.001 # keep OTUs that are found in at least 30% of samples cutoff = .3 use.mat <- kgct.filtered.classified.list[[tax.level]]@mat