GenomeDataList-class {BSgenome} | R Documentation |
GenomeDataList
is a list of
GenomeData
objects. It could be useful for
storing data on multiple experiments or samples.
This class inherits from SimpleList
and requires
that all of its elements to be instances of GenomeData
.
One should try to take advantage of the metadata storage facilities
provided by SimpleList
. The elementMetadata
field,
for example, could be used to store the experimental design, while
the metadata
field could store the experimental platform.
GenomeDataList(listData = list(), metadata = list(),
elementMetadata = NULL)
:
Creates a GenomeDataList
with the elements from the
listData
parameter, a list of GenomeData
instances. The other arguments correspond to the optional metadata
stored in SimpleList
.
as(from, "data.frame")
: Coerces each subelement to a
data frame, and binds them into a single data frame with an
additional column indicating chromosome
gdreduce(f, ..., init, right=FALSE, accumulate=FALSE, gdArgs=list())
:
Currently this method works when a single GenomeDataList
is
provided as ...
. It successively combines the
GenomeData
elements in the
GenomeDataList
using f
. f
is a function
accepting two objects returned by "[["
applied to the
successive GenomeData
elements of ...
, returning a
single GenomeData
object to be used in subsequent calls to
f
. init
, right
, and accumulate
are as
described for Reduce
. gdArgs
can be used to
provide metadata information to the constructor used to create the
final GenomeData
object.
Michael Lawrence
GenomeData, the type of elements stored in this class. SimpleList
gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)), organism = "Mmusculus", provider = "UCSC", providerVersion = "mm9") gdl <- GenomeDataList(list(gd), elementMetadata = DataFrame(induced = TRUE)) gdl[[1]] # get first element gdr <- gdreduce(function(x, y) { ## "[[" returns IRanges instances, construct a synthetic version IRanges(c(start(x), start(y)), c(end(x), end(y))) }, GenomeDataList(list(gd, gd[2]))) gdr[["chr1"]] gdr[["chrX"]]