From 8ac158251475b2f3ae081783d82d77ec909cb370 Mon Sep 17 00:00:00 2001 From: hyginn Date: Wed, 22 Nov 2017 12:05:02 -0500 Subject: [PATCH] TRUE and FALSE were inverted in explanation of masking --- BIN-PHYLO-Data_preparation.R | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/BIN-PHYLO-Data_preparation.R b/BIN-PHYLO-Data_preparation.R index f18e759..21f6a6b 100644 --- a/BIN-PHYLO-Data_preparation.R +++ b/BIN-PHYLO-Data_preparation.R @@ -188,16 +188,17 @@ colMask <- logical(ncol(msaMatrix)) limit <- round(nrow(APSESMsa) * (2/3)) # iterate over all columns, and write TRUE if there are less-or-equal to "limit" -# hyphens, FALSE if there are more. +# hyphens, FALSE if there are more - i.e. TRUE columns will be used fr analysis +# and FALSE columns will be rejected. for (i in 1:ncol(msaMatrix)) { count <- sum(msaMatrix[ , i] == "-") - colMask[i] <- count <= limit # FALSE if less-or-equal to limit, TRUE if not + colMask[i] <- count <= limit # TRUE if less-or-equal to limit, FALSE if not } -# inspect the mask +# Inspect the mask colMask -# How many positions were masked? +# How many positions are being kept? sum(colMask) cat(sprintf("We are masking %4.2f %% of alignment columns.\n",