-
Notifications
You must be signed in to change notification settings - Fork 12
/
seqDigest.Rd
52 lines (45 loc) · 1.25 KB
/
seqDigest.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
47
48
49
50
51
52
\name{seqDigest}
\alias{seqDigest}
\title{Hash function digests}
\description{
Create hash function digests for all or a subset of data
}
\usage{
seqDigest(gdsfile, varname, algo=c("md5"), verbose=FALSE)
}
\arguments{
\item{gdsfile}{a \code{\link{SeqVarGDSClass}} object}
\item{varname}{the variable name(s), see details}
\item{algo}{the digest hash algorithm: "md5"}
\item{verbose}{if \code{TRUE}, show progress information}
}
\details{
The variable name should be \code{"sample.id"}, \code{"variant.id"},
\code{"position"}, \code{"chromosome"}, \code{"allele"}, \code{"annotation/id"},
\code{"annotation/qual"}, \code{"annotation/filter"},
\code{"annotation/info/VARIABLE_NAME"}, or
\code{"annotation/format/VARIABLE_NAME"}.
Users can define a subset of data via \code{\link{seqSetFilter}} and
create a hash digest for the subset only.
}
\value{
A hash character.
}
\author{Xiuwen Zheng}
\seealso{
\code{\link{seqSetFilter}}, \code{\link{seqApply}}
}
\examples{
# the GDS file
(gds.fn <- seqExampleFileName("gds"))
# display
f <- seqOpen(gds.fn)
seqDigest(f, "genotype")
seqDigest(f, "annotation/filter")
seqDigest(f, "annotation/format/DP")
# close the GDS file
seqClose(f)
}
\keyword{gds}
\keyword{sequencing}
\keyword{genetics}