BamFileViews: Views into a set of BAM files

Description

This class is deprecated. Use GenomicFiles instead. Use BamFileViews() to reference a set of disk-based BAM files to be processed

Constructor

: BamFileViews(fileList, fileSample=DataFrame(row.names=make.unique(basename(path(fileList)))), fileRange, fileExperiment = list(), yieldSize = NA_integer_, .views_on_file = new.env(parent=emptyenv()), ...): This constructor is a generic function with dispatch on argument fileList. Methods exist for BamFileList and character (vector of file names).

Accessors

All accessor-like methods defined for GenomicFileViews objects work on BamFileViews objects. See ?GenomicFileViews for details.

fileList(x); fileList(x) <- value
fileSample(x); fileSample(x) <- value
fileRange(x); fileRange(x) <- value
fileExperiment(x); fileExpermient(x) <- value
yieldSize(x); yieldSize(x) <- value

Methods

: "[": Subset the object by fileRange or fileSample.
reduceByFile: Computations are distributed in parallel by files in fileList with the option to provide MAP and REDUCE functions across ranges and / or files.
reduceByRange: Computations are distributed in parallel by ranges in fileRange with the option to provide MAP and REDUCE functions across ranges and / or files.
summarizeOverlaps: Computations are distributed in parallel by files in fileList. Ranges in the fileRange slot take precedence over ranges in param. The return value is a SummarizedExperiment object.
countBam: Computations are distributed in parallel by files in fileList. Ranges in the fileRange slot take precedence over ranges in param. The return value is a list of data.frames, one per file.
scanBam: Computations are distributed in parallel by files in fileList. Ranges in the fileRange slot take precedence over ranges in param. The return value is a list of lists, one per file.

Arguments

: fileList: A character() vector of BAM path names or a BamFileList.
: fileSample: A DataFrame instance with as many rows as length(fileList), containing sample information associated with each path.
: fileRange: A GRanges, or missing instance with ranges defined on the spaces of the BAM files. Ranges are not validated against the BAM files.
: fileExperiment: A list() containing additional information about the experiment.
: yieldSize: An integer specifying number of records to process
: .views_on_file: An enviornment; currently under development
: ...: Additional arguments.
: x, object: An instance of BamFileViews.
: value: An object of appropriate type to replace content.
: i: During subsetting, a logical or numeric index into fileRange.
: j: During subsetting, a logical or numeric index into fileSample and fileList.
: file: An instance of BamFileViews.
: index: Not used.
: param: An optional ScanBamParam instance to further influence scanning or counting.

Slots

Inherited from GenomicFileViews class:

fileList
fileSample
fileRange
fileExperiment
yieldSize
.views_on_file

Examples

Run this code

library(RNAseqData.HNRNPC.bam.chr14)
fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES
gr <- GRanges("chr14", IRanges(1:10*5, width = 2))
bfv <- BamFileViews(fls, fileRange = gr)

## Dimensions of the object are ranges by samples (files).
bfv 
bfv[1:5,]
fileList(bfv)
fileRange(bfv)

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