View source: R/func__getGeneClasses.R
getGeneClass | R Documentation |
SRST2 defines each allele ID using several fields: [sequence cluster ID]__[cluster symbol (the name of a gene, product class or group)]__[gene or allele name]__[sequence ID] [additional annotations separated by ";"]. For instance, a valid sequence ID is: 225__SulI_Sul__SulI__1616 no;no;SulI;Sul;U37105;4069-4908;840. Usually, the cluster symbol is the antimicrobial class for an antimicrobial resistance gene. This function aims to extract this symbol from the allele ID. It is a simple function, however, this package includes it because of its frequent usage.
getGeneClass(ids)
ids |
A character vector of allele IDs. |
Yu Wan (wanyuac@126.com)
assoc <- lmm(...) arg_cls <- data.frame(allele = assoc$mapping$allele, class = getGeneClass(x = assoc$mapping$gene), stringsAsFactors = FALSE)
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