-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathhlaSampleAllele.Rd
46 lines (42 loc) · 1.34 KB
/
hlaSampleAllele.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
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
\name{hlaSampleAllele}
\alias{hlaSampleAllele}
\title{
Get sample IDs from HLA types with a filter
}
\description{
Get sample IDs from HLA types limited to a set of HLA alleles.
}
\usage{
hlaSampleAllele(TrueHLA, allele.limit=NULL, max.resolution="")
}
\arguments{
\item{TrueHLA}{an object of \code{\link{hlaAlleleClass}}}
\item{allele.limit}{a list of HLA alleles, the validation samples are
limited to those having HLA alleles in \code{allele.limit}, or
\code{NULL} for no limit. \code{allele.limit} could be character-type,
\code{\link{hlaAttrBagClass}} or \code{\link{hlaAttrBagObj}}}
\item{max.resolution}{"2-digit", "4-digit", "6-digit", "8-digit", "allele",
"protein", "2", "4", "6", "8", "full" or "": "allele" = "2-digit",
"protein" = "4-digit", "full" and "" mean no limit on resolution}
}
\value{
Return a list of sample IDs.
}
\author{Xiuwen Zheng}
\seealso{
\code{\link{hlaCompareAllele}}
}
\examples{
# make a "hlaAlleleClass" object
hla.id <- "A"
hla <- hlaAllele(HLA_Type_Table$sample.id,
HLA_Type_Table[, paste(hla.id, ".1", sep="")],
HLA_Type_Table[, paste(hla.id, ".2", sep="")],
locus=hla.id, assembly="hg19")
summary(hla)
hlaSampleAllele(hla)
hlaSampleAllele(hla, allele.limit=c(
"01:01","02:01","02:06", "03:01", "11:01", "23:01"))
}
\keyword{HLA}
\keyword{genetics}