Hm, I tried a dirty hack: I exported the DNAbin object using ape::write.dna and replaced all occurrences of "n" in any sequence by "-" and imported the file back to R with ape::read.dna. Then I tried the mentioned functions. They did nothing. When I exported the file to disk, the FASTA file did not contain any "-", only "n". DO I do something wrong, or is there a bug in ape as it seems to confuse "n" and "-"? Sincerely, V.
Dne pátek 27. října 2017 16:25:02 CEST jste napsal(a):
> Hello,
> 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
> threshold).
> 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?
> Sincerely,
> V.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University, Prague, Czech Republic
https://www.natur.cuni.cz/biology/botany/
Institute of Botany, Czech Academy of Sciences
Průhonice, Czech Republic
http://www.ibot.cas.cz/en/
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