Rsamtools: ScanBcfParam-class – R documentation

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ScanBcfParam-class

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 `ScanVcfParam` only.
`info`	A character() vector of ‘INFO’ fields (see scanVcfHeader) to be returned.
`geno`	A character() vector of ‘GENO’ fields (see scanVcfHeader) to be returned. `character(0)` returns all fields, `NA_character_` returns none.
`samples`	A character() vector of sample names (see scanVcfHeader) to be returned. `character(0)` returns all fields, `NA_character_` returns none.
`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 `POS` lies in the interval(s) `[start, end)` are returned.
`object`	An instance of class `ScanBcfParam`.
`...`	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 with ScanVcfParam only.

Functions and methods

See 'Usage' for details on invocation.

Constructor:

ScanBcfParam:: Returns a ScanBcfParam object. The which 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

Examples

## see ?ScanVcfParam examples

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

v2.6.0

Artistic-2.0 | file LICENSE

Authors

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden

Initial release