Hi, I have my data in a fasta file and am importing it into R using read.dna, which creates a DNAbin matrix object. I would like to subset my file depending on the sequence name so that I can generate the nucleotide pairwise distance using dist.dna. I have attempted to do this using grep, but all I get is a list of the numbers of the sequences with the correct name and no sequences or sequence names. Does anyone have a suggestions for an easy way to do this?
For example, my DNAbin object has the following row names: [1] "01011-DNA1.Contig1" "01011-DNA11.Contig1" "01011-DNA12.Contig1" "01011-DNA13.Contig1" "01011-DNA14.Contig1" [6] "01011-DNA16.Contig1" "01011-DNA17.Contig1" "01011-DNA18.Contig1" "01011-DNA19.Contig1" "01011-DNA2.Contig1" [11] "01011-DNA20.Contig1" "01011-DNA21.Contig1" "01011-DNA22.Contig1" "01011-DNA23.Contig1" "01011-DNA24.Contig1" [16] "01011-DNA25.Contig1" "01011-DNA26.Contig1" "0103-PRNA2.Contig1" "01011-DNA3.Contig1" "01011-DNA33.Contig1" [21] "01011-DNA4.Contig1" "01011-DNA5.Contig1" "01011-DNA6.Contig1" "01011-DNA7.Contig1" "01011-DNA8.Contig1" [26] "01011-DNA9.Contig1" "01011-RNA10.Contig1" "01011-RNA13.Contig1" "01011-RNA14.Contig1" "01011-RNA17.Contig1" [31] "01011-RNA18.Contig1" "01011-RNA19.Contig1" "01011-RNA21.Contig1" "01011-RNA23.Contig1" "01011-RNA24.Contig1" [36] "01011-RNA26.Contig1" "01011-RNA28.Contig1" "01011-RNA29.Contig1" "01011-RNA30.Contig1" "01011-RNA31.Contig1" [41] "01011-RNA32.Contig1" "01011-RNA33.Contig1" "01011-RNA35.Contig1" "01011-RNA38.Contig1" "01011-RNA4.Contig1" [46] "01011-RNA5.Contig1" "01011-RNA6.Contig1" "01011-RNA8.Contig1" "01011-RNA9.Contig1" "0102A-CRNA103.Contig1" [51] "0102A-CRNA105.Contig1" "0102A-CRNA110.Contig1" "0102A-CRNA113.Contig1" "0102A-CRNA115.Contig1" "0102A-CRNA118.Contig1" [56] "0102a-DNA10.Contig1” I would like a new DNAbin object with sequences that have 1011 anywhere in their row name. Please let me know if i have left out any pertinent information. Thank you in advance for any suggestions or help with this matter. Kind regards, Kirston _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
