annotation {rRDP} | R Documentation |
Functions to represent, decode and encode phylogenetic classification annotations used in FASTA files by RDP and the Greengenes project.
GenClass16S(Kingdom=NA, Phylum=NA, Class=NA, Order=NA, Family=NA, Genus=NA, Species=NA, Otu=NA, Org_name=NA, Id=NA) decode_RDP(annotation) encode_RDP(classification) decode_Greengenes(annotation) encode_Greengenes(classification)
Kingdom |
Name of the kingdom to which the organism belongs. |
Phylum |
Name of the phylum to which the organism belongs. |
Class |
Name of the class to which the organism belongs. |
Order |
Name of the order to which the organism belongs. |
Family |
Name of the family to which the organism belongs. |
Genus |
Name of the genus to which the organism belongs. |
Species |
Name of the species to which the organism belongs. |
Otu |
Name of the otu to which the organism belongs. |
Org_name |
Name of the organism. |
Id |
ID of the sequence. |
annotation |
Annotation from a FASTA file containing the classification information. |
classification |
A |
GenClass16S()
and decodeX()
return a data.frame
.
encodeX()
returns a string with the corresponding annotation.
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta", package="rRDP")) ### the FASTA annotation is read as names. This data has a Greengenes format ### annotation names(seq) classification <- decode_Greengenes(names(seq)) classification ### look at the Genus of all sequences classification[, "Genus"] ### to train the RDP classifier, the annotations need to be in RDP format annotation <- encode_RDP(classification) names(seq) <- annotation seq ### now we can train the classifier customRDP <- trainRDP(seq) customRDP ## clean up removeRDP(customRDP)