RaggedExperiment-class {RaggedExperiment} | R Documentation |
The RaggedExperiment
class is a container for
storing range-based data, including but not limited to copy
number data, and mutation data. It can store a collection of
GRanges
objects, as it is derived from the
GenomicRangesList
.
RaggedExperiment(..., colData = DataFrame()) ## S4 method for signature 'RaggedExperiment' rowRanges(x, ...) ## S4 method for signature 'RaggedExperiment' dim(x) ## S4 method for signature 'RaggedExperiment' dimnames(x) ## S4 replacement method for signature 'RaggedExperiment,list' dimnames(x) <- value ## S4 method for signature 'RaggedExperiment' colData(x, ...) ## S4 replacement method for signature 'RaggedExperiment,DataFrame' colData(x) <- value ## S4 method for signature 'RaggedExperiment,missing' assay(x, i, ...) ## S4 method for signature 'RaggedExperiment,ANY' assay(x, i, ..., withDimnames = TRUE) ## S4 method for signature 'RaggedExperiment' assays(x, ..., withDimnames = TRUE) ## S4 method for signature 'RaggedExperiment' assayNames(x, ...) ## S4 method for signature 'RaggedExperiment' show(object) ## S4 method for signature 'RaggedExperiment,ANY,ANY,ANY' x[i, j, ..., drop = TRUE] ## S4 method for signature 'RaggedExperiment,Vector' overlapsAny(query, subject, maxgap = 0L, minoverlap = 1L, type = c("any", "start", "end", "within", "equal"), ...) ## S4 method for signature 'RaggedExperiment,Vector' subsetByOverlaps(x, ranges, maxgap = -1L, minoverlap = 0L, type = c("any", "start", "end", "within", "equal"), invert = FALSE, ...)
... |
Constructor: GRanges, list of GRanges, or GRangesList OR assay: Additional arguments for assay. See details for more information. |
colData |
A |
x |
A RaggedExperiment object. |
value |
A |
i |
logical(1), integer(1), or character(1) indicating the
assay to be reported. For |
withDimnames |
logical (default TRUE) whether to use dimension names in the resulting object |
object |
A RaggedExperiment object. |
j |
integer(), character(), or logical() index selecting columns from RaggedExperiment |
drop |
logical (default TRUE) whether to drop empty samples |
query |
A RaggedExperiment instance. |
subject |
Each of them can be a Ranges, Views, RangesList,
or ViewsList object.
In addition, if If If both arguments are list-like objects with names, each list element from the 2nd argument is paired with the list element from the 1st argument with the matching name, if any. Otherwise, list elements are paired by position. The overlap is then computed between the pairs as described below. If |
maxgap |
A single integer >= -1. If If |
minoverlap |
A single non-negative integer. Only ranges with a minimum of When |
type |
By default, any overlap is accepted. By specifying the The |
ranges |
Each of them can be a Ranges, Views, RangesList,
or ViewsList object.
In addition, if If If both arguments are list-like objects with names, each list element from the 2nd argument is paired with the list element from the 1st argument with the matching name, if any. Otherwise, list elements are paired by position. The overlap is then computed between the pairs as described below. If |
invert |
If |
constructor returns a RaggedExperiment
object
'rowRanges' returns a GRanges
object
summarizing ranges corresponding to assay()
rows.
'assays' returns a SimpleList
overlapsAny
returns a logical vector of length equal
to the number of rows in the query
; TRUE
when the
copy number region overlaps the subject
.
subsetByOverlaps
returns a RaggedExperiment containing
only copy number regions overlapping subject
.
rowRanges
: rowRanges accessor
dim
: get dimensions (number of sample-specific row
ranges by number of samples)
dimnames
: get row (sample-specific) range names
and sample names
dimnames<-
: set row (sample-specific) range names
and sample names
colData
: get column data
colData<-
: change the colData
assay
: assay missing method uses first metadata column
assay
: assay numeric method.
assays
: assays
assayNames
: names in each assay
show
: show method
[
: Subset a RaggedExperiment object
overlapsAny
: Determine whether copy number ranges
defined by query
overlap ranges of subject
.
subsetByOverlaps
: Subset the RaggedExperiment to contain only
copy number ranges overlapping ranges of subject
.
RaggedExperiment(..., colData=DataFrame())
: Creates a
RaggedExperiment object using multiple GRanges
objects or a list
of GRanges
objects. Additional column data may be provided
as a DataFrame
object.
In the following, 'x' represents a RaggedExperiment
object:
x[i, j]
: Get ranges or elements (i
and j
,
respectively) with optional metadata columns where i
or j
can be missing, an NA-free logical, numeric, or character vector.
Coercion possible from
RangedRaggedAssay to
RaggedExperiment. Here object
represents a
RangedRaggedAssay
: as(object, "RaggedExperiment")
## Create an empty RaggedExperiment instance re0 <- RaggedExperiment() re0 ## Create a couple of GRanges objects with row ranges names sample1 <- GRanges( c(a = "chr1:1-10:-", b = "chr1:11-18:+"), score = 1:2) sample2 <- GRanges( c(c = "chr2:1-10:-", d = "chr2:11-18:+"), score = 3:4) ## Include column data colDat <- DataFrame(id = 1:2) ## Create a RaggedExperiment object from a couple of GRanges re1 <- RaggedExperiment(sample1=sample1, sample2=sample2, colData = colDat) re1 ## With list of GRanges lgr <- list(sample1 = sample1, sample2 = sample2) ## Create a RaggedExperiment from a list of GRanges re2 <- RaggedExperiment(lgr, colData = colDat) grl <- GRangesList(sample1 = sample1, sample2 = sample2) ## Create a RaggedExperiment from a GRangesList re3 <- RaggedExperiment(grl, colData = colDat) ## Subset a RaggedExperiment assay(re3[c(1, 3),]) subsetByOverlaps(re3, GRanges("chr1:1-5")) # by ranges