Thank You, Andreas, yes, I try to manipulate an alignment. This is nice trick, although it returns empty alignment regardless threshold value used (I do have some data in the alignment:-)... Have a nice weekend, V.
Dne pátek 27. října 2017 17:02:45 CEST jste napsal(a):
> Hello V.
> Because you speak of columns I assume you are handling an alignment,
> right? If you handle an alignment all sequences have the same length and
> you can do as.matrix
>
> Like this?
>
> library(magrittr)
> #maximum number of n's
> thresh <- 0.005 #0.5%
> seq <- as.matrix(seq)
> temp <- seq %>% sapply(.,grep,pattern="n") %>% unlist(.,use.names=F) %>%
> table
> seq[,-(names(temp)[which(temp/ncol(seq)>thresh)] %>% as.integer)]
>
> Greetings,
> Andreas
>
> Am 2017-10-27 16:25, schrieb Vojtěch Zeisek:
> > 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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