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

See Also

scanVcf

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]