Description Constructor Details Accessors Methods Author(s) See Also Examples
The GenomicFiles
class is a matrix-like container where rows
represent ranges of interest and columns represent files. The class
is designed for byFile or byRange queries.
GenomicFiles(rowRanges, files, colData=DataFrame(),
metadata=list(), ...)
:
GenomicFiles
inherits from the RangedSummarizedExperiment
class in the SummarizedExperiment
package. Currently, no use
is made of the elementMetadat
and assays
slots. This may
change in the future.
In the code below, x
is a GenomicFiles object.
Get or set the rowRanges on x
. value
can be
a GRanges
or GRangesList
representing ranges or indices
defined on the spaces (position) of the files.
Get or set the files on x
. value
can be
a character() of file paths or a List of file objects
such as BamFile, BigWigFile, FaFile, etc.
Get or set the colData on x
. value
must be
a DataFrame
instance describing the files. The number
of rows must match the number of files. Row names, if present,
become the column names of the GenomicFiles
.
Get or set the metadata on x
. value
must be
a SimpleList of arbitrary content describing the overall
experiment.
Get or set the row and column names on x
.
In the code below, x
is a GenomicFiles object.
Subset the object by fileRange
or fileSample
.
Compactly display the object.
Extract, manipulate and combine data defined in rowRanges
within the files specified in files
. See ?reduceByFile
for details.
Extract, manipulate and combine data defined in rowRanges
across the files specified in files
. See ?reduceByRange
for details.
Martin Morgan and Valerie Obenchain
reduceByFile and reduceByRange methods.
SummarizedExperiment objects in the SummarizedExperiment package.
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## Basic Use
## -----------------------------------------------------------------------
if (require(RNAseqData.HNRNPC.bam.chr14)) {
fl <- RNAseqData.HNRNPC.bam.chr14_BAMFILES
rd <- GRanges("chr14",
IRanges(c(62262735, 63121531, 63980327), width=214700))
cd <- DataFrame(method=rep("RNASeq", length(fl)),
format=rep("bam", length(fl)))
## Construct an instance of the class:
gf <- GenomicFiles(files = fl, rowRanges = rd, colData = cd)
gf
## Subset on ranges or files for different experimental runs.
dim(gf)
gf_sub <- gf[2, 3:4]
dim(gf_sub)
## When summarize = TRUE and no REDUCE is provided the reduceBy*
## functions output a SummarizedExperiment object.
MAP <- function(range, file, ...) {
requireNamespace("GenomicFiles", quietly=TRUE) ## for coverage()
requireNamespace("Rsamtools", quietly=TRUE) ## for ScanBamParam()
param = Rsamtools::ScanBamParam(which=range)
GenomicFiles::coverage(file, param=param)[range]
}
se <- reduceByRange(gf, MAP=MAP, summarize=TRUE)
se
## Data from the rowRanges, colData and metadata slots in the
## GenomicFiles are transferred to the SummarizedExperiment.
colData(se)
## Results are in the assays slot.
assays(se)
}
## -----------------------------------------------------------------------
## Managing cached or remote files with GenomicFiles
## -----------------------------------------------------------------------
## The GenomicFiles class can manage cached or remote files and their
## associated ranges.
## Not run:
## Files from AnnotationHub can be downloaded and cached locally.
library(AnnotationHub)
hub = AnnotationHub()
hublet = query(hub, c("files I'm", "interested in"))
# cache (if need) and return local path to files
fls = cache(hublet)
## An alternative to the local file paths is to use urls to a remote file.
## This approach could be used with something like rtracklayer::bigWig which
## supports remote file queries.
urls = hublet$sourceurls
## Define ranges of interest and use GenomicFiles to manage.
rngs = GRanges("chr10", IRanges(c(100000, 200000), width=1))
gf = GenomicFiles(rngs, fls)
## As an example, one could create a matrix from data extracted
## across multiple BED files.
MAP = function(rng, fl) {
requireNamespace("rtracklayer", quietly=TRUE) ## import, BEDFile
rtracklayer::import(rtracklayer::BEDFile(fl), which=rng)$name
}
REDUCE = unlist
xx = reduceFiles(gf, MAP=MAP, REDUCE=REDUCE)
mcols(rngs) = simplify2array(xx)
## Data and ranges can be stored in a SummarizedExperiment.
SummarizedExperiment(list(my=simplify2array(xx)), rowRanges=rngs)
## End(Not run)
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