FaFileViews() to reference a set of disk-based Fasta files to be
processed
FaFileViews(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 FaFileList and character
(vector of file names).
GenomicFileViews objects
work on FaFileViews objects. See ?GenomicFileViews for details.
"[": Subset the object by fileRange or fileSample.
fileList
with the option to provide MAP and REDUCE functions across ranges
and / or files.
fileRange
with the option to provide MAP and REDUCE functions across ranges
and / or files.
fileList:
A character() vector of Fasta path names or a
FaFileList.
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 Fasta files. Ranges are
not validated against the Fasta files.
fileExperiment:
A list() containing additional information about the experiment.
yieldSize: An integer specifying number of records to process
.views_on_file: An environment; currently under development
...: Additional arguments.
x, object: An instance of FaFileViews.
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 FaFileViews.
index: Not used.
param:
Unused option for FaFileViews object. fileRange
are used to specify ranges to query.
GenomicFileViews class:
fa <- system.file("extdata", "ce2dict1.fa", package="Rsamtools",
mustWork=TRUE)
ffv <- FaFileViews(c(fa, fa), fileRange=scanFaIndex(fa))
ffv
Run the code above in your browser using DataLab