GenomicFiles (version 1.4.0)

GenomicFileViews: Views into a set of files

Description

This class is deprecated. 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.

See Also

• BamFileViews-class class.
• BigWigFileViews-class class.
• reduceByFile and reduceFiles methods.
• reduceByRange and reduceRanges methods.

Examples

if (require(RNAseqData.HNRNPC.bam.chr14)) { 
  fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES
  gr <- GRanges("chr14", IRanges(c(62262735, 63121531, 63980327),
                width=214700))
 
  ## The GenomicFiles class is a light-weight form of SummarizedExperiment
  ## with no 'assays' slot. 
  colData <- DataFrame(method=rep("RNASeq", length(fls)),
                       format=rep("bam", length(fls)))
  gf <- GenomicFiles(files=fls, rowData=gr, colData=colData)
  gf

  ## The object can be subset on ranges or files for different
  ## experimental runs.
  dim(gf)
  gf_sub <- gf[2, 3:4]
  dim(gf_sub)
}