I checked ape::del.colgapsonly, ips::deleteGaps and ips::deleteEmptyCells. 
They delete columns containing missing values, but I need also to delete 
columns containing base "N" (all columns with amount of Ns over certain 
Actually, ips::deleteEmptyCells has option nset=c("-", "n", "?"), so it is 
suppose to remove columns/rows containing only the given characters, but if I 
use it and export data (ape::write.dna or ape::write.nexus.data), some samples 
consist only of N characters...
The DNAbin object being processed was originally imported from VCF using vcfR 
(read.vcfR(file="my.vcf") and converted: vcfR2DNAbin(x=myvcf, consensus=TRUE, 
extract.haps=FALSE, unphased_as_NA=FALSE)).
I checked source code of the above functions, but they seem to only count NAs 
and then drop respective columns. And as sequences in DNAbin are stored in 
binary format, I'm bit struggled here... :(
Any idea how to remove columns with given portion of "N" in sequences?

Vojtěch Zeisek

Department of Botany, Faculty of Science
Charles University, Prague, Czech Republic

Institute of Botany, Czech Academy of Sciences
Průhonice, Czech Republic

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