R: Parameters for scanning VCF / BCF files

ScanBcfParam-class {Rsamtools}

R Documentation

Parameters for scanning VCF / BCF files

Description

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.

Usage


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)

Arguments

`info`	A character() vector of ‘INFO’ fields (see `scanVcfHeader`) to be returned. Not currently implemented.
`geno`	A character() vector of ‘GENO’ fields (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. Methods defined for `ScanBcfParam` are available for `ScanVcfParam`.
`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 "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.

Functionas and methods

See 'Usage' for details on invocation.

Constructor:

ScanVcfParam, ScanBcfParam:: Returns a ScanVcfParam or 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

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)

[Package Rsamtools version 1.6.3 Index]