Gallery - Example 8

Below is the R code to reproduce the example:

Hide output

library(DECIPHER)
Loading required package: Biostrings
Loading required package: BiocGenerics


Attaching package: ‘BiocGenerics’


The following objects are masked from ‘package:stats’:


	IQR, mad, sd, var, xtabs


The following objects are masked from ‘package:base’:


	anyDuplicated, aperm, append,
	as.data.frame, basename, cbind,
	colnames, dirname, do.call, duplicated,
	eval, evalq, Filter, Find, get, grep,
	grepl, intersect, is.unsorted, lapply,
	Map, mapply, match, mget, order, paste,
	pmax, pmax.int, pmin, pmin.int,
	Position, rank, rbind, Reduce, rownames,
	sapply, setdiff, table, tapply, union,
	unique, unsplit, which.max, which.min


Loading required package: S4Vectors
Loading required package: stats4


Attaching package: ‘S4Vectors’


The following object is masked from ‘package:utils’:


	findMatches


The following objects are masked from ‘package:base’:


	expand.grid, I, unname


Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb


Attaching package: ‘Biostrings’


The following object is masked from ‘package:base’:


	strsplit


> 
> load("GTDB_r220-mod_April2024.RData", verbose=TRUE)
Loading objects:
trainingSet
> 
> # import test sequences
> fas <- system.file("extdata", "Bacteria_175seqs.fas", package="DECIPHER")
> dna <- readDNAStringSet(fas)
> 
> # remove any gaps in the sequences
> dna <- RemoveGaps(dna)
> 
> # classify the test sequences
> ids <- IdTaxa(dna, trainingSet, strand="top", processors=NULL)
|========================================| 100%


Time difference of 13.42 secs


> ids
A test set of class 'Taxa' with length 175
	confidence name                 taxon
[1]        79% uncultured bacter... Root; Bac...
[2]        91% uncultured bacter... Root; Bac...
[3]        94% uncultured bacter... Root; Bac...
[4]        95% uncultured bacter... Root; Bac...
[5]        60% uncultured bacter... Root; Bac...
...        ... ...                  ...
[171]        41% uncultured bacter... Root; unc...
[172]        87% uncultured bacter... Root; Bac...
[173]        33% uncultured bacter... Root; unc...
[174]        56% uncultured bacter... Root; unc...
[175]        59% uncultured bacter... Root; unc...
> 
> # view the results
> plot(ids)