R: Class '"refSeqDict"': Repesentation of data from reference...

refSeqDict-class {rbamtools} | R Documentation

## Class `"refSeqDict"`: Repesentation of data from reference sequence dictionary in BAM file header.

### Description

refSeqDict 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("refSeqDict")`.

### Slots

`SN`:

  character

`LN`:

  numeric

`AS`:

  character

`M5`:

  numeric

`SP`:

  character

`UR`:

  character

### Methods

dim

  `signature(x="refSeqDict")`: Returns dimension of data: number of rows and 6 columns.

as.data.frame

  `signature(object="refSeqDict")`: Combines data of Slots to data.frame.

coerce

  `signature(from="bamRange", to="data.frame")`: Coercion of refSeqDice to data.frame.

removeSeqs

  `signature(object="refSeqDict",rows="numeric")`: Removes reference sequence (i.e. one row from data.frame) entry.

addSeq

  `signature(.Object="refSeqDict",SN,LN,AS,M5,SP,UR)`: Adds reference sequence (i.e. one row in data.frame) entry.

head

  `signature(.Object="refSeqDict",n)`: Returns head of data.frame representation.

tail

  `signature(.Object="refSeqDict",n)`: Returns tail of data.frame representation.

getHeaderText

  `signature(.Object="refSeqDict")`: Returns textual representation of data stored in this class as desrcribed in SAM Format Specification.

### 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)
    refSeqs<-refSeqDict(htxt)
    dim(refSeqs)
    ht<-getHeaderText(refSeqs)
    df<-as.data.frame(refSeqs)
    addSeq(refSeqs,SN="nextSeqName",LN=1000)
    removeSeqs(refSeqs,3)
    bamClose(reader)

[Package rbamtools version 2.16.17 Index]