R: Class '"headerReadGroup"': Representation of read - group...

headerReadGroup-class {rbamtools} | R Documentation

## Class `"headerReadGroup"`: Representation of read - group data in header section of BAM files

### Description

headerReadGroup represents data contained in the header section of BAM-files.

### Objects from the Class

Objects can be created by calls of the form `hl<-new("headerReadGroup")`.

### Slots

`nrg`:

  `integer`. Number of read groups.

`ntl`:

  `integer`. Number of different read group tags (currently = 12).

`ID`:

  `character`. Read group identifier. Each read group must have an unique ID.

`CN`:

  `character`. Name of sequencing center.

`DS`:

  `character`. Description.

`DT`:

  `character`. Date of run.

`FO`:

  `character`. Flow order.

`KS`:

  `character`. Array of nucleotide bases.

`LB`:

  `character`. Library.

`PG`:

  `character`. Programs used for processing.

`PI`:

  `character`. Predicted median insert size.

`PL`:

  `character`. Platform/technology for production of reads.

`PU`:

  `character`. Unique platform identifier.

`SM`:

  `character`. Sample name.

### Methods

addReadGroup

  `signature(object="headerReadGroup", l="list")`: Adds new read group to object.

as.list

  `signature(x="headerReadGroup")`: Returns data stored in this object as list.

getVal

  `signature(object="headerReadGroup")`: Returns value of given segment.

setVal

  `signature(object="headerReadGroup")`: Sets value of given segment.

getHeaderText

  `signature(.Object="headerReadGroup")`: Returns textual representation of data as specified in SAM Format.

### Author(s)

Wolfgang Kaisers

### References

`The SAM Format Specification (v1.4-r985). The SAM Format Specification Working Group. September 7, 2011.`

### Examples

    bam <- system.file("extdata", "accepted_hits.bam", package="rbamtools")
    reader<-bamReader(bam)
    isOpen(reader)
    header<-getHeader(reader)
    htxt<-getHeaderText(header)
    readGroup<-headerProgram(htxt)
    getVal(readGroup,"ID")
    setVal(readGroup,"ID","newID")
    l<-as.list(readGroup)
    txt<-getHeaderText(readGroup)
    bamClose(reader)

[Package rbamtools version 2.16.17 Index]