pubmlst-package: pubmlst

In jmarshallnz/pubmlst: Infer Sequence Types Based On Allelic Profiles

Description

Infer Sequence Types Based On Allelic Profiles

Details

Utilises the database from PubMLST (http://pubmlst.org) to infer sequence types and species given an allelic profile for Campylobacter jejuni and coli. Imputes missing alleles if present.

Author(s)

Jonathan Marshall

References

http://pubmlst.org

Examples

# impute missing alleles, sequence type etc.
df <- data.frame(id=c("A", "B"), ASP=c(2,2), GLN=c(1,4), GLT=c(54,1), 
                 GLY=c(NA, 2), PGM=c(4,2), TKT=c(1,1), UNC=c(5,NA))
impute_mlst_in_data(df)

# take a look at the PubMLST data
head(pubmlst)

jmarshallnz/pubmlst documentation built on Nov. 16, 2020, 2:44 a.m.