GenomicFileViews: Views into a set of files

Description

GenomicFileViews is a VIRTUAL class used to reference a set of disk-based files to be queried across views (ranges).

Arguments

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.

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.

Examples

Run this code

fl <- system.file("extdata", "ex1.bam", package="Rsamtools",
                  mustWork=TRUE) 
bfv <- BamFileViews(fl, fileRange = GRanges("seq1", IRanges(1, 10)))
showClass(class(bfv))
 
## See ?BamFileViews, ?BigWigFileViews, ?reduceBy for additional examples.

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