GenomicFileViews: Views into a set of files
Description
This class is defunct. Use GenomicFiles instead.
GenomicFileViews is a VIRTUAL class used to reference a set of
disk-based files to be queried across views (ranges).
Objects from the Class
GenomicFileViews is a VIRTUAL class not intended for instantiation by
the user. The class serves as a parent for concrete subclasses such
as BamFileViews, FaFileViews, TabixFileViews etc.Slots
- fileList
-
List of of length >= 2 containing the file path and index names.
List names must include ‘path’ and ‘index’.
- fileSample
-
A DataFrame instance with as many rows as
length(fileList), containing sample information associated
with each path.
- fileRange
-
A
GRanges instance with ranges defined
on the spaces (genomic position) of the files.
- fileExperiment
-
A
list containing additional information about the experiment.
- yieldSize
-
An integer specifying the data chunk size.
- .views_on_file
-
An environment. Under construction / future use.
Accessors
In the code snippets below, x is a GenomicFileViews object.
itemfileList(x), fileList(x) <- value
Get or set the fileList on x. value must be
a List with list elements appropriate for the subclass. - fileSample, fileSample(x) <- value
-
Get or set the fileSample on
x. value must be
a DataFrame instance with as many rows as
length(fileList), containing sample information associated
with each file.
- fileRange, fileRange(x) <- value
-
Get or set the fileSample on
x. value must be
a GRanges instance.
- fileExperiment, fileExperiment(x) <- value
-
Get or set the fileExperiment on
x. value must be
a list().
- yieldSize, yieldSize(x) <- value
-
Get or set the yieldSize on
x. value must be
an integer.
- names, names(x) <- value
-
Get or set the names on
x. These are the column
names of the GenomicFileViews instance corresponding to
the paths in fileList.
- dimnames, dimnames(x) <- value
-
Get or set the row and column names on
x.
Methods
In the code snippets below, x is a GenomicFileViews object.
- [
-
Subset the object by
fileRange or fileSample.
- show
-
Compactly display the object.
- reduceByFile
-
Parallel computations are distributed by files in
fileList
with the option to provide MAP and REDUCE functions across ranges
and / or files.
- reduceByRange
-
Parallel computations are distributed by ranges in
fileRange
with the option to provide MAP and REDUCE functions across ranges
and / or files.