GenomicFiles instead.
Use BigWigFileViews() to reference a set of disk-based BigWig files
to be processed (e.g., queried using coverage) as
a single ‘experiment’.
BigWigFileViews(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
BigWigFileList and character()
(vector of file names).
GenomicFileViews objects
work on BigWigFileViews objects. See ?GenomicFileViews for details.
"[": Subset the object by fileRange or fileSample.
x and object are
BigWigFileViews objects. coverage(x, ..., by = "file", summarize = TRUE,
as = "RleList"):
Computes coverage with the import function from
rtracklayer for each file in fileList(x) and
each range in fileRange(x). Work is divided
in parallel as specified in the by argument. Results
are returned as a list unless summarize=TRUE in
which case the data are in the assays slot of
a SummarizedExperiment object. Data type are controlled with
the as argument. See ?'import,BigWigFile-method'
for details.
summary(object, ..., by = "file", summarize = TRUE):
Computes summary statistics with the summary function
from rtracklayer for each file in fileList(object)
and each range in fileRange(object). Work is divided in
parallel as specified in the by argument. Results are
returned as a list unless summarize=TRUE in which case the
data are in the assays slot of a SummarizedExperiment
object. Summary statistics are controlled with the type
argument passed to summary. See
?'summary,BigWigFile-method' for details.
fileList:
A character() vector of BigWig path names or a
BigWigFileList.
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 BigWig files. Ranges are
not validated against the BigWig 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 BigWigFileViews.
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 BigWigFileViews.
index: Not used.
GenomicFileViews class: