ScanBcfParam-class {Rsamtools} | R Documentation |
Parameters for scanning BCF files
Description
Use ScanBcfParam()
to create a parameter object influencing the
‘INFO’ and ‘GENO’ fields parsed, and which sample records are
imported from a BCF file. Use of which
requires that a BCF
index file (<filename>.bci
) exists.
Usage
ScanBcfParam(fixed=character(), info=character(), geno=character(),
samples=character(), trimEmpty=TRUE, which, ...)
## S4 method for signature 'missing'
ScanBcfParam(fixed=character(), info=character(), geno=character(),
samples=character(), trimEmpty=TRUE, which, ...)
## S4 method for signature 'IntegerRangesList'
ScanBcfParam(fixed=character(), info=character(), geno=character(),
samples=character(), trimEmpty=TRUE, which, ...)
## S4 method for signature 'GRanges'
ScanBcfParam(fixed=character(), info=character(), geno=character(),
samples=character(), trimEmpty=TRUE, which, ...)
## S4 method for signature 'GRangesList'
ScanBcfParam(fixed=character(), info=character(), geno=character(),
samples=character(), trimEmpty=TRUE, which, ...)
## Accessors
bcfFixed(object)
bcfInfo(object)
bcfGeno(object)
bcfSamples(object)
bcfTrimEmpty(object)
bcfWhich(object)
Arguments
fixed |
A logical(1) for use with |
info |
A character() vector of ‘INFO’ fields (see scanVcfHeader) to be returned. |
geno |
A character() vector of ‘GENO’ fields (see
scanVcfHeader) to be returned. |
samples |
A character() vector of sample names (see
scanVcfHeader) to be returned. |
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 from the Class
Objects can be created by calls of the form ScanBcfParam()
.
Slots
which
:Object of class
"IntegerRangesList"
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.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.fixed
:Object of class
"character"
. For use withScanVcfParam
only.
Functions and methods
See 'Usage' for details on invocation.
Constructor:
- ScanBcfParam:
Returns a
ScanBcfParam
object. Thewhich
argument to the constructor can be one of several types, as documented above.
Accessors:
- bcfInfo, bcfGeno, bcfTrimEmpty, bcfWhich:
Return the corresponding field from
object
.
Methods:
- show
Compactly display the object.
Author(s)
Martin Morgan mtmorgan@fhcrc.org
See Also
Examples
## see ?ScanVcfParam examples