ScanBcfParam-class {Rsamtools} | R Documentation |
Use ScanBcfParam()
to create a parameter object influencing the
‘INFO’ and ‘GENO’ fields parsed, and which recrods are
imported from a BCF file. Use of which
requires that a BCF
index file (<filename>.bci
) exists.
ScanBcfParam(info=character(), geno=character(), trimEmpty=TRUE, which, ...) ## S4 method for signature 'missing' ScanBcfParam(info=character(), geno=character(), trimEmpty=TRUE, which, ...) ## S4 method for signature 'RangesList' ScanBcfParam(info=character(), geno=character(), trimEmpty=TRUE, which, ...) ## S4 method for signature 'RangedData' ScanBcfParam(info=character(), geno=character(), trimEmpty=TRUE, which, ...) ## S4 method for signature 'GRanges' ScanBcfParam(info=character(), geno=character(), trimEmpty=TRUE, which, ...) ScanVcfParam(info=character(), geno=character(), trimEmpty=TRUE, which, ...) ## Accessors bcfInfo(object) bcfGeno(object) bcfTrimEmpty(object) bcfWhich(object) vcfInfo(object) vcfGeno(object) vcfTrimEmpty(object) vcfWhich(object)
info |
A character() vector of ‘INFO’ fields (see
|
geno |
A character() vector of ‘GENO’ fields (see
|
trimEmpty |
A logical(1) indicating whether ‘GENO’ fields with no values should be returned. |
which |
An object, for which a method is defined (see usage,
above), describing the sequences and ranges to be queried. Variants
whose |
object |
An instance of class |
... |
Arguments used internally. |
Objects can be created by calls of the form ScanBcfParam()
.
which
:Object of class "RangesList"
indicating
which reference sequence and coordinate variants must overlap.
info
:Object of class "character"
indicating
portions of ‘INFO’ to be returned.
geno
:Object of class "character"
indicating
portions of ‘GENO’ 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
or
ScanBcfParam
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 mtmorgan@fhcrc.org
p0 <- ScanVcfParam() ## subset of reads based on genomic coordinates which <- RangesList(seq1=IRanges(1000, 2000), seq2=IRanges(c(100, 1000), c(1000, 2000))) p1 <- ScanVcfParam(which=which) ## return only specified GENO field(s) p2 <- ScanVcfParam(geno="GT", which=which)