getRefData: Retrieve reference sequence from a BAM file as data.frame

In rbamtools: Read and Write BAM (Binary Alignment) Files

Description

The four functions: getRefCoords, getRefCount, getRefData and getRefId provide reading access to data about the present reference sequences in bamReader or bamWriter.

Usage

getRefData(object)

Arguments

object

bamReader. The reader must be opened (otherwise an error is thrown).

Details

getRefData returns a data.frame with three columns (ID, SN, LN). ID is the (0-based index which must be given when a bamRange is extracted. SN is the name of the sequence (e.g. chr1 for UCSC). LN is the length of the reference sequence. getRefCount returns the number of reference sequences. getRefCoords returns a vector of coordinates which can be used to extract all stored aligns for this sequence from the bamReader into a bamRange object.

Author(s)

Wolfgang Kaisers

Examples

bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
reader<-bamReader(bam,idx=TRUE)
getRefData(reader)
getRefCount(reader)
getRefId(reader, "chr1")
coords<-getRefCoords(reader, "chr1")
rg<-bamRange(reader,coords)
bamClose(reader)

Example output

Loading required package: refGenome
Loading required package: doBy
Loading required package: RSQLite
  ID    SN        LN
1  0  chr1 249250621
2  1 chr16  90354753
[1] 2
[1] 0

rbamtools documentation built on Nov. 11, 2019, 5:09 p.m.