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TRUE and FALSE were inverted in explanation of masking

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hyginn 2017-11-22 12:05:02 -05:00
parent 5e4ecbaf6f
commit 8ac1582514
1 changed files with 5 additions and 4 deletions
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9
BIN-PHYLO-Data_preparation.R
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@ -188,16 +188,17 @@ colMask <- logical(ncol(msaMatrix))
limit <- round(nrow(APSESMsa) * (2/3)) limit <- round(nrow(APSESMsa) * (2/3))
# iterate over all columns, and write TRUE if there are less-or-equal to "limit" # 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)) { for (i in 1:ncol(msaMatrix)) {
count <- sum(msaMatrix[ , i] == "-") 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 colMask
# How many positions were masked? # How many positions are being kept?
sum(colMask) sum(colMask)
cat(sprintf("We are masking %4.2f %% of alignment columns.\n", cat(sprintf("We are masking %4.2f %% of alignment columns.\n",