# Create and Manipulate Locus, Gene, and Marker Objects `locus`, `gene`, and `marker` create objects to store information, respectively, about genetic loci, genes, and markers. `is.locus`, `is.gene`, and `ismarker` test whether an object is a member of the respective class. `as.character.locus`, `as.character.gene`, `as.character.marker` return a character string containing a compact encoding the object. `getlocus`, `getgene`, `getmarker` extract locus data (if present) from another object. `locus<-`, `marker<-`, and `gene<-` adds locus data to an object. ```r locus(name, chromosome, arm=c("p", "q", "long", "short", NA), index.start, index.end=NULL) gene(name, chromosome, arm=c("p", "q", "long", "short"), index.start, index.end=NULL) marker(name, type, locus.name, bp.start, bp.end = NULL, relative.to = NULL, ...) is.locus(x) is.gene(x) is.marker(x) ## S3 method for class 'locus' as.character(x, ...) ## S3 method for class 'gene' as.character(x, ...) ## S3 method for class 'marker' as.character(x, ...) getlocus(x, ...) locus(x) <- value marker(x) <- value gene(x) <- value ``` ## Arguments - `name`: character string giving locus, gene, or marker name - `chromosome`: integer specifying chromosome number (1:23 for humans). - `arm`: character indicating long or short arm of the chromosome. Long is be specified by "long" or "p". Short is specified by "short" or "q". - `index.start`: integer specifying location of start of locus or gene on the chromosome. - `index.end`: optional integer specifying location of end of locus or gene on the chromosome. - `type`: character string indicating marker type, e.g. "SNP" - `locus.name`: either a character string giving the name of the locus or gene (other details may be specified using `...`) or a `locus` or `gene` object. - `bp.start`: start location of marker, in base pairs - `bp.end`: end location of marker, in base pairs (optional) - `relative.to`: location (optional) from which `bp.start` and `bp.end` are calculated. - `...`: parameters for `locus` used to fill in additional details on the locus or gene within which the marker is located. - `x`: an object of class `locus`, `gene`, or `marker`, or (for `getlocus`, `locus<-`, `marker<-`, and `gene<-`) an object that may contain a locus attribute or field, notably a `genotype` object. - `value`: `locus`, `marker`, or `gene` object ## Returns Object of class `locus` and `gene`are lists with the elements: - **name**: character string giving locus, gene, or marker name - **chromosome**: integer specifying chromosome number (1:23 for humans). - **arm**: character indicating long or short arm of the chromosome. Long is be specified by "long" or "p". Short is specified by "short" or "q". - **index.start**: integer specifying location of start of locus or gene on the chromosome. - **index.end**: optional integer specifying location of end of locus or gene on the chromosome. Objects of class `marker` add the additional fields: - **marker.name**: character string giving the name of the marker - **bp.start**: start location of marker, in base pairs - **bp.end**: end location of marker, in base pairs (optional) - **relative.to**: location (optional) from which `bp.start` and `bp.end` are calculated. ## Author(s) Gregory R. Warnes greg@warnes.net ## See Also `genotype`, ## Examples ```r ar2 <- gene("AR2",chromosome=7,arm="q",index.start=35) ar2 par <- locus(name="AR2 Psedogene", chromosome=1, arm="q", index.start=32, index.end=42) par c109t <- marker(name="C-109T", type="SNP", locus.name="AR2", chromosome=7, arm="q", index.start=35, bp.start=-109, relative.to="start of coding region") c109t c109t <- marker(name="C-109T", type="SNP", locus=ar2, bp.start=-109, relative.to="start of coding region") c109t example.data <- c("D/D","D/I","D/D","I/I","D/D", "D/D","D/D","D/D","I/I","") g1 <- genotype(example.data, locus=ar2) g1 getlocus(g1) summary(g1) HWE.test(g1) g2 <- genotype(example.data, locus=c109t) summary(g2) getlocus(g2) heterozygote(g2) homozygote(g1) allele(g1,1) carrier(g1,"I") heterozygote(g2) ```

locus function