Description usage arguments Objects from the Class Fields Functions and methods Author(s) Examples
Use VcfFile()
to create a reference to a Vcf file (and its
index). Once opened, the reference remains open across calls to
methods, avoiding costly index re-loading.
VcfFileList()
provides a convenient way of managing a list of
VcfFile
instances.
## Constructors
VcfFile(file, index = paste(file, "tbi", sep="."), ..., yieldSize=NA_integer_)
VcfFileList(..., yieldSize=NA_integer_)
## Accessors
index(object)
path(object, ...)
isOpen(con, rw="")
yieldSize(object, ...)
yieldSize(object, ...) <- value
show(object)
## Opening / closing
open(con, ...)
close(con, ...)
## method
vcfFields(object)
conAn instance of VcfFile
.
fileA character(1) vector to the Vcf file path; can be remote (http://, ftp://).
indexA character(1) vector of the Vcf file index (.tbi file).
yieldSizeNumber of records to yield each time the file is read
from using scanVcf
or readVcf
.
...Additional arguments. For VcfFileList
, this can
either be a single character vector of paths to Vcf files, or
several instances of VcfFile
objects.
rwcharacter() indicating mode of file.
Objects are created by calls of the form VcfFile()
.
VcfFile
and VcfFileList
classes inherit fields from the
TabixFile
and TabixFileList
classes.
VcfFile
and VcfFileList
classes inherit methods from the
TabixFile
and TabixFileList
classes.
## Opening / closing:
Opens the (local or remote) path
and
index
. Returns a VcfFile
instance.
yieldSize
determines the number of records parsed during
each call to scanVcf
or readVcf
; NA
indicates
that all records are to be parsed.
Closes the VcfFile
con
; returning
(invisibly) the updated VcfFile
. The instance may be
re-opened with open.VcfFile
.
## Accessors:
Returns a character(1) vector of the Vcf path name.
Returns a character(1) vector of Vcf index (tabix file) name.
Return or set an integer(1) vector indicating yield size.
## Methods:
Returns a CharacterList
of all available VCF
fields, with names of fixed
, info
, geno
and
samples
indicating the four categories. Each element is a
character() vector of available VCF field names within each
category. It works for both local and remote vcf file.
Valerie Obenchain
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | fl <- system.file("extdata", "chr7-sub.vcf.gz", package="VariantAnnotation",
mustWork=TRUE)
vcffile <- VcfFile(fl)
vcffile
vcfFields(fl)
vcfFields(vcffile)
param <- GRanges("7", IRanges(c(55000000, 55900000), width=10000))
vcf <- readVcf(vcffile, "hg19", param=param)
dim(vcf)
## `vcfFields` also works for remote vcf filepath.
## Not run:
chr22url <- "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"
vcfFields(chr22url)
## End(Not run)
|
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