Description Usage Arguments Details Author(s) Examples
The three functions: getRefCoords
, getRefCount
and getRefData
provide reading access to data about the present reference sequences in the bamHeader.
1 | getRefData(object)
|
object |
|
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.
Wolfgang Kaisers
1 2 3 4 5 6 7 | bam<-system.file("extdata","accepted_hits.bam",package="rbamtools")
reader<-bamReader(bam,idx=TRUE)
getRefData(reader)
getRefCount(reader)
coords<-getRefCoords(reader,"chr1")
rg<-bamRange(reader,coords)
bamClose(reader)
|
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