bacteria {ade4}R Documentation

Genomes of 43 Bacteria

Description

bacteria is a list containing 43 species and genomic informations : codons, amino acid and bases.

Usage

data(bacteria)

Format

This list contains the following objects:

code
is a factor with the amino acid names for each codon.
espcodon
is a data frame 43 species 64 codons.
espaa
is a data frame 43 species 21 amino acid.
espbase
is a data frame 43 species 4 bases.

Source

Data prepared by J. Lobry lobry@biomserv.univ-lyon1.fr starting from:
http://www.tigr.org/tdb/mdb/mdbcomplete.html

Examples

data(bacteria)
names(bacteria$espcodon)
names(bacteria$espaa)
names(bacteria$espbase)
sum(bacteria$espcodon) # 22,619,749 codons
scatter.coa(dudi.coa(bacteria$espcodon, scann = FALSE), 
    posi = "bottom")

Worked out examples


> library(ade4)
> ### Name: bacteria
> ### Title: Genomes of 43 Bacteria
> ### Aliases: bacteria
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(bacteria)
> names(bacteria$espcodon)
 [1] "GCT" "GCC" "GCA" "GCG" "CGT" "CGC" "CGA" "CGG" "AGA" "AGG" "AAT" "AAC"
[13] "GAT" "GAC" "TGT" "TGC" "CAA" "CAG" "GAA" "GAG" "GGT" "GGC" "GGA" "GGG"
[25] "CAT" "CAC" "ATT" "ATC" "ATA" "TTA" "TTG" "CTT" "CTC" "CTA" "CTG" "AAA"
[37] "AAG" "ATG" "TTT" "TTC" "CCT" "CCC" "CCA" "CCG" "TCT" "TCC" "TCA" "TCG"
[49] "AGT" "AGC" "TAA" "TAG" "TGA" "ACT" "ACC" "ACA" "ACG" "TGG" "TAT" "TAC"
[61] "GTT" "GTC" "GTA" "GTG"
> names(bacteria$espaa)
 [1] "Ala" "Arg" "Asn" "Asp" "Cys" "Gln" "Glu" "Gly" "His" "Ile" "Leu" "Lys"
[13] "Met" "Phe" "Pro" "Ser" "Stp" "Thr" "Trp" "Tyr" "Val"
> names(bacteria$espbase)
[1] "A" "C" "G" "T"
> sum(bacteria$espcodon) # 22,619,749 codons
[1] 22619749
> scatter.coa(dudi.coa(bacteria$espcodon, scann = FALSE), 
+     posi = "bottom")
> 
> 
> 
> 

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