Description Usage Arguments Objects from the Class Slots Functions and methods Author(s) See Also Examples
Use ScanVcfParam()
to create a parameter object influencing
which records and fields are imported from a VCF file. Record
parsing is based on genomic coordinates and requires a Tabix index
file. Individual VCF elements can be specified in the ‘fixed’,
‘info’, ‘geno’ and ‘samples’ arguments.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ScanVcfParam(fixed=character(), info=character(), geno=character(),
samples=character(), trimEmpty=TRUE, which, ...)
## Getters and Setters
vcfFixed(object)
vcfFixed(object) <- value
vcfInfo(object)
vcfInfo(object) <- value
vcfGeno(object)
vcfGeno(object) <- value
vcfSamples(object)
vcfSamples(object) <- value
vcfTrimEmpty(object)
vcfTrimEmpty(object) <- value
vcfWhich(object)
vcfWhich(object) <- value
|
fixed |
A character() vector of fixed fields to be returned. Possible
values are ALT, QUAL and FILTER. The CHROM, POS, ID and REF fields are
needed to create the |
info |
A character() vector naming the ‘INFO’ fields to return.
|
geno |
A character() vector naming the ‘GENO’ fields to return.
|
samples |
A character() vector of sample names to return.
|
trimEmpty |
A logical(1) indicating whether ‘GENO’ fields with no values should be returned. |
which |
A |
object |
An instance of class |
value |
An instance of the corresponding slot, to be assigned to
|
... |
Arguments passed to methods. |
Objects can be created by calls of the form ScanVcfParam()
.
which
:Object of class "IntegerRangesList"
indicating
which reference sequence and coordinate variants must overlap.
fixed
:Object of class "character"
indicating
fixed fields to be returned.
info
:Object of class "character"
indicating
portions of ‘INFO’ to be returned.
geno
:Object of class "character"
indicating
portions of ‘GENO’ to be returned.
samples
:Object of class "character"
indicating
the samples to be returned.
trimEmpty
:Object of class "logical"
indicating
whether empty ‘GENO’ fields are to be returned.
See 'Usage' for details on invocation.
Constructor:
Returns a ScanVcfParam
object.
The which
argument to the constructor can be one of several types,
as documented above.
Accessors:
Return the corresponding field from object
.
Methods:
Compactly display the object.
Martin Morgan and Valerie Obenchain
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 | ScanVcfParam()
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
compressVcf <- bgzip(fl, tempfile())
idx <- indexTabix(compressVcf, "vcf")
tab <- TabixFile(compressVcf, idx)
## ---------------------------------------------------------------------
## 'which' argument
## ---------------------------------------------------------------------
## To subset on genomic coordinates, supply an object
## containing the ranges of interest. These ranges can
## be given directly to the 'param' argument or wrapped
## inside ScanVcfParam() as the 'which' argument.
## When using a list, the outer list names must correspond to valid
## chromosome names in the vcf file. In this example they are "1"
## and "2".
gr1 <- GRanges("1", IRanges(13219, 2827695, name="regionA"))
gr2 <- GRanges(rep("2", 2), IRanges(c(321680, 14477080),
c(321689, 14477090), name=c("regionB", "regionC")))
grl <- GRangesList("1"=gr1, "2"=gr2)
vcf <- readVcf(tab, "hg19", grl)
## Names of the ranges are in the 'paramRangeID' metadata column of the
## GRanges object returned by the rowRanges() accessor.
rowRanges(vcf)
## which can be used for subsetting the VCF object
vcf[rowRanges(vcf)$paramRangeID == "regionA"]
## When using ranges, the seqnames must correspond to valid
## chromosome names in the vcf file.
gr <- unlist(grl, use.names=FALSE)
vcf <- readVcf(tab, "hg19", gr)
## ---------------------------------------------------------------------
## 'fixed', 'info', 'geno' and 'samples' arguments
## ---------------------------------------------------------------------
## This param specifies the "GT" 'geno' field for a single sample
## and the subset of ranges in 'which'. All 'fixed' and 'info' fields
## will be returned.
ScanVcfParam(geno="GT", samples="NA00002", which=gr)
## Here two 'fixed' and one 'geno' field are specified
ScanVcfParam(fixed=c("ALT", "QUAL"), geno="GT", info=NA)
## Return only the 'fixed' fields
ScanVcfParam(geno=NA, info=NA)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.