PileupFiles | R Documentation |
Use PileupFiles()
to create a reference to BAM files (and
their indicies), to be used for calculating pile-up summaries.
## Constructors
PileupFiles(files, ..., param=ApplyPileupsParam())
## S4 method for signature 'character'
PileupFiles(files, ..., param=ApplyPileupsParam())
## S4 method for signature 'list'
PileupFiles(files, ..., param=ApplyPileupsParam())
## opening / closing
## open(con, ...)
## close(con, ...)
## accessors; also path()
## S4 method for signature 'PileupFiles'
isOpen(con, rw="")
plpFiles(object)
plpParam(object)
## actions
## S4 method for signature 'PileupFiles,missing'
applyPileups(files, FUN, ..., param)
## S4 method for signature 'PileupFiles,ApplyPileupsParam'
applyPileups(files, FUN, ..., param)
## display
## S4 method for signature 'PileupFiles'
show(object)
files |
For For |
... |
Additional arguments, currently ignored. |
con , object |
An instance of |
FUN |
A function of one argument; see |
param |
An instance of |
rw |
character() indicating mode of file; not used for
|
Objects are created by calls of the form PileupFiles()
.
The PileupFiles
class is implemented as an S4 reference
class. It has the following fields:
A list of BamFile
instances.
An instance of ApplyPileupsParam
.
Opening / closing:
Opens the (local or remote) path
and
index
of each file in the PileupFiles
instance. Returns a PileupFiles
instance.
Closes each file in the PileupFiles
instance; returning (invisibly) the updated
PileupFiles
. The instance may be re-opened with
open.PileupFiles
.
Accessors:
Returns the list
of the files in the
PileupFiles
instance.
Returns the ApplyPileupsParam
content of the
PileupFiles
instance.
Methods:
Calculate the pileup across all files in
files
according to criteria in param
(or
plpParam(files)
if param
is missing), invoking
FUN
on each range or collection of positions. See
applyPileups
.
Compactly display the object.
Martin Morgan
example(applyPileups)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.