-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathhlaSNPGenoClass.Rd
28 lines (26 loc) · 994 Bytes
/
hlaSNPGenoClass.Rd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
\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}