hlaSNPGenoClass.Rd

\name{hlaSNPGenoClass}
\alias{hlaSNPGenoClass}
\title{The class of SNP genotypes}
\description{
    The class of SNP genotypes, and its instance is returned from
\code{\link{hlaMakeSNPGeno}}.
}
\value{
    There are five components:
    \item{genotype}{a genotype matrix, ``# of SNPs''-by-``# of individuals'';
        0 standing for BB (ZERO A allele), 1 for AB (ONE A allele), 2 for AA
        (TWO A alleles) and NA for missing values (other values have no meaning)}
    \item{sample.id}{a vector of sample IDs}
    \item{snp.id}{a vector of SNP IDs}
    \item{snp.position}{a vector of SNP positions in basepair}
    \item{snp.allele}{a vector of characters with a format of ``A allele/B allele'';
        B is usually defined as a major or reference allele, while A is defined as
        a minor or alternative allele}
    \item{assembly}{the human genome reference, such like "hg19"}
}

\author{Xiuwen Zheng}
\seealso{
    \code{\link{hlaMakeSNPGeno}}
}

\keyword{SNP}
\keyword{genetics}