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 `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

### See Also

scanVcf ScanVcfParam

### Examples

    ## see ?ScanVcfParam examples

[Package Rsamtools version 2.6.0 Index]