I used the classify.seqs with the silva.archaea database on a my sequences and tried to remove unclassifed sequences at the kingdom level (i.e. sequences that are not archaea). The problem is that when I put unclassified in taxon:
remove.lineage(fasta=arch.trim.contigs.good.unique.good.filter.unique.precluster.pick.abund.fasta, count=arch.trim.contigs.good.unique.good.filter.unique.precluster.uchime.pick.abund.count_table, taxonomy=arch.trim.contigs.good.unique.good.filter.unique.precluster.pick.abund.silva.wang.taxonomy, taxon=unclassified)
the remove.lineage function removed all unclassified sequences (due to poor taxonomic classification in archaea, most sequences are unclassified after the phylum or class level), not only at the kingdom level. Is there a way to remove lineage based on rank.ID?
Thank in advance