|
Last data update: 2014.03.03
|
R: A base class for managing file references in Rsamtools
| RsamtoolsFile | R Documentation |
A base class for managing file references in Rsamtools
Description
RsamtoolsFile is a base class for managing file references in
Rsamtools; it is not intended for direct use by users – see, e.g.,
BamFile.
Usage
## accessors
index(object)
## S4 method for signature 'RsamtoolsFile'
path(object, ...)
## S4 method for signature 'RsamtoolsFile'
isOpen(con, rw="")
## S4 method for signature 'RsamtoolsFile'
yieldSize(object, ...)
yieldSize(object, ...) <- value
## S4 method for signature 'RsamtoolsFile'
show(object)
Arguments
con, object |
An instance of a class derived from RsamtoolsFile.
|
rw |
Mode of file; ignored.
|
... |
Additional arguments, unused.
|
value |
Replacement value.
|
Objects from the Class
Users do not directly create instances of this class; see, e.g.,
BamFile-class.
Fields
The RsamtoolsFile class is implemented as an S4 reference
class. It has the following fields:
- .extptr
An externalptr initialized to an internal
structure with opened bam file and bam index pointers.
- path
A character(1) vector of the file name.
- index
A character(1) vector of the index file name.
- yieldSize
An integer(1) vector of the number of records to
yield.
Functions and methods
Accessors:
- path
Returns a character(1) vector of path names.
- index
Returns a character(1) vector of index path names.
- yieldSize, yieldSize<-
Return or set an integer(1) vector
indicating yield size.
Methods:
- isOpen
Report whether the file is currently open.
- show
Compactly display the object.
Author(s)
Martin Morgan
Results
|
providing 
.