RangedSummarizedExperiment-class
RangedSummarizedExperiment objects
The RangedSummarizedExperiment class is a matrix-like container where rows represent ranges of interest (as a GRanges or GRangesList object) and columns represent samples (with sample data summarized as a DataFrame). A RangedSummarizedExperiment contains one or more assays, each represented by a matrix-like object of numeric or other mode.
RangedSummarizedExperiment is a subclass of SummarizedExperiment and,
as such, all the methods documented in ?SummarizedExperiment
also work on a RangedSummarizedExperiment object. The methods documented
below are additional methods that are specific to RangedSummarizedExperiment
objects.
Usage
## Constructor
SummarizedExperiment(assays, ...)
"SummarizedExperiment"(assays, rowData=NULL, rowRanges=GRangesList(), colData=DataFrame(), metadata=list())
"SummarizedExperiment"(assays, ...)
"SummarizedExperiment"(assays, ...)
"SummarizedExperiment"(assays, ...)
## Accessors
rowRanges(x, ...)
rowRanges(x, ...) <- value
## Subsetting
"subset"(x, subset, select, ...)
## rowRanges access
## see 'GRanges compatibility', belowArguments
- assays
- A
listorSimpleListof matrix-like elements, or a matrix-like object. All elements of the list must have the same dimensions, and dimension names (if present) must be consistent across elements and with the row names ofrowRangesandcolData. - rowData
- A DataFrame object describing
the rows. Row names, if present, become the row names of the
SummarizedExperiment object. The number of rows of the
DataFrame must equal the number of rows of the
matrices in
assays. - rowRanges
- A GRanges or
GRangesList object describing the ranges of
interest. Names, if present, become the row names of the
SummarizedExperiment object. The length of the
GRanges or GRangesList
must equal the number of rows of the matrices in
assays. IfrowRangesis missing, a SummarizedExperiment instance is returned. - colData
- An optional DataFrame describing the samples. Row names, if present, become the column names of the RangedSummarizedExperiment.
- metadata
- An optional
listof arbitrary content describing the overall experiment. - ...
- For
SummarizedExperiment, S4 methodslistandmatrix, arguments identical to those of theSimpleListmethod.For
rowRanges, ignored. - x
- A RangedSummarizedExperiment object. The
rowRangessetter will also accept a SummarizedExperiment object and will first coerce it to RangedSummarizedExperiment before it setsvalueon it. - value
- A GRanges or GRangesList object.
- subset
- An expression which, when evaluated in the
context of
rowRanges(x), is a logical vector indicating elements or rows to keep: missing values are taken as false. - select
- An expression which, when evaluated in the
context of
colData(x), is a logical vector indicating elements or rows to keep: missing values are taken as false.
Details
The rows of a RangedSummarizedExperiment object represent ranges
(in genomic coordinates) of interest. The ranges of interest are
described by a GRanges or a GRangesList object, accessible
using the rowRanges function, described below. The GRanges
and GRangesList classes contains sequence (e.g., chromosome) name,
genomic coordinates, and strand information. Each range can be
annotated with additional data; this data might be used to describe
the range or to summarize results (e.g., statistics of differential
abundance) relevant to the range. Rows may or may not have row names;
they often will not.
Constructor
RangedSummarizedExperiment instances are constructed using the
SummarizedExperiment function with arguments outlined above.
Accessors
In the following code snippets, x is a RangedSummarizedExperiment
object.
rowRanges(x),rowRanges(x) <- value:- Get or set the
row data.
valueis aGenomicRangesobject. Row names ofvaluemust be NULL or consistent with the existing row names ofx.
GRanges compatibility (rowRanges access)
Many GRanges and GRangesList operations are supported on
RangedSummarizedExperiment objects, using rowRanges. Supported operations include: pcompare,
duplicated, end, end<-,
granges, is.unsorted, match,
mcols, mcols<-, order,
ranges, ranges<-, rank,
seqinfo, seqinfo<-, seqnames,
sort, start, start<-,
strand, strand<-,
width, width<-. See also ?shift,
?isDisjoint,
?coverage,
?findOverlaps, and
?nearest for more
GRanges compatibility methods. Not all GRanges operations are supported, because
they do not make sense for RangedSummarizedExperiment objects
(e.g., length, name, as.data.frame, c, splitAsList), involve
non-trivial combination or splitting of rows (e.g., disjoin, gaps,
reduce, unique), or have not yet been implemented (Ops, map, window,
window<-).
Subsetting
In the code snippets below, x is a RangedSummarizedExperiment
object.
subset(x, subset, select):- Create a subset of
xusing an expressionsubsetreferring to columns ofrowRanges(x)(including ‘seqnames’, ‘start’, ‘end’, ‘width’, ‘strand’, andnames(rowData(x))) and / orselectreferring to column names ofcolData(x).
Extension
RangedSummarizedExperiment is implemented as an S4 class, and can be
extended in the usual way, using contains="RangedSummarizedExperiment"
in the new class definition.
See Also
- SummarizedExperiment objects.
- shift,
isDisjoint,
coverage,
findOverlaps, and
nearest for more
GRanges compatibility methods.
- GRanges objects in the GenomicRanges package.
Examples
nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
IRanges(floor(runif(200, 1e5, 1e6)), width=100),
strand=sample(c("+", "-"), 200, TRUE),
feature_id=sprintf("ID%03d", 1:200))
colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
row.names=LETTERS[1:6])
rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
rowRanges=rowRanges, colData=colData)
rse
dim(rse)
dimnames(rse)
assayNames(rse)
head(assay(rse))
assays(rse) <- endoapply(assays(rse), asinh)
head(assay(rse))
rowRanges(rse)
rowData(rse) # same as 'mcols(rowRanges(rse))'
colData(rse)
rse[, rse$Treatment == "ChIP"]
## cbind() combines objects with the same ranges but different samples:
rse1 <- rse
rse2 <- rse1[,1:3]
colnames(rse2) <- letters[1:ncol(rse2)]
cmb1 <- cbind(rse1, rse2)
dim(cmb1)
dimnames(cmb1)
## rbind() combines objects with the same samples but different ranges:
rse1 <- rse
rse2 <- rse1[1:50,]
rownames(rse2) <- letters[1:nrow(rse2)]
cmb2 <- rbind(rse1, rse2)
dim(cmb2)
dimnames(cmb2)
## Coercion to/from SummarizedExperiment:
se0 <- as(rse, "SummarizedExperiment")
se0
as(se0, "RangedSummarizedExperiment")
## Setting rowRanges on a SummarizedExperiment object turns it into a
## RangedSummarizedExperiment object:
se <- se0
rowRanges(se) <- rowRanges
se # RangedSummarizedExperiment
## Sanity checks:
stopifnot(identical(assays(se0), assays(rse)))
stopifnot(identical(dim(se0), dim(rse)))
stopifnot(identical(dimnames(se0), dimnames(rse)))
stopifnot(identical(rowData(se0), rowData(rse)))
stopifnot(identical(colData(se0), colData(rse)))