Description Usage Arguments Value Examples
Functions to represent, decode and encode phylogenetic classification annotations used in FASTA files by RDP and the Greengenes project.
1 2 3 4 5 6 7 | 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | 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)
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