BamSampler {Rsamtools} | R Documentation |
Use BamSampler()
to create a reference to a BAM file (and
optionally its index). Calls to scanBam
(and many functions
that use scanBam
) draw a random sample from the BAM file.
## Constructors BamSampler(file, index = file, ..., yieldSize, obeyQname = FALSE, asMates = FALSE) ## S4 method for signature 'BamSampler' scanBam(file, index=file, ..., param=ScanBamParam(what=scanBamWhat()))
file |
character(1); BAM file path for |
index |
character(1); the BAM index file path (for
|
... |
Additional arguments; see |
yieldSize |
integer(1); number of records to yield each time the
file is read from using |
obeyQname |
logical(1); indicating whether the file is sorted by
|
asMates |
logical(1); indicating whether the records should be returned as mated pairs. |
param |
An optional |
Objects are created by calls of the form BamSampler()
.
The BamSampler
class inherits fields from the
BamFile
class.
BamSampler
inherits methods from BamFile
and can
be used in place of BamFile
in many functions.
Martin Morgan
library(GenomicAlignments) # for readGAlignmentsFromBam() fl <- system.file("extdata", "ex1.bam", package="Rsamtools") samp <- BamSampler(fl, yieldSize=1000) ## two independent samples head(readGAlignmentsFromBam(samp)) head(readGAlignmentsFromBam(samp))