1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
|
\name{makeSummarizedExperimentFromLoom}
\alias{makeSummarizedExperimentFromLoom}
\title{Make a SummarizedExperiment from a '.loom' hdf5 file}
\description{
\code{makeSummarizedExperimentFromLoom} represents a '.loom' file as
a \code{SummarizedExperiment}. The \code{'/matrix'} and
\code{'/layers'} are represented as \code{HDF5Array} objects; row
and column attributes are parsed to \code{DataFrame}. Optionally,
row or column attributes can be specified as row and and column
names.
}
\usage{
makeSummarizedExperimentFromLoom(file,
rownames_attr = NULL,
colnames_attr = NULL)
}
\arguments{
\item{file}{
The path (as a single character string) to the HDF5 file where
the dataset is located.
}
\item{rownames_attr}{
The name of the row attribute to be used as row names.
}
\item{colnames_attr}{
The name of the column attribute to be used as column names.
}
}
\value{
A \link{SummarizedExperiment} object with row and column data and
one or more assays.
}
\author{
Martin Morgan
}
\seealso{
\url{http://loompy.org/loompy-docs/format/index.html} for a
specification of the .loom format.
}
\examples{
## ---------------------------------------------------------------------
## BASIC EXAMPLE
## ---------------------------------------------------------------------
file <- system.file(
package="SummarizedExperiment", "extdata", "example.loom"
)
se <- makeSummarizedExperimentFromLoom(file)
se
assay(se)
metadata(se)
}
|
