add_rse: Method to add a 'RangedSummarizedExperiment' to...

In MultiDataSet: Implementation of MultiDataSet and ResultSet

Description

This method adds or overwrites a slot of a MultiDataSet with the content of the given RangedSummarizedExperiment.

Usage

add_rse(
  object,
  set,
  dataset.type,
  dataset.name = NULL,
  sample.tables = NULL,
  feature.tables = NULL,
  warnings = TRUE,
  overwrite = FALSE
)

Arguments

object	MultiDataSet that will be filled.
set	Object derived from RangedSummarizedExperiment to be used to fill the slot.
dataset.type	Character with the type of data of the omic set (e.g. expression, methylation...)
dataset.name	Character with the specific name for this set (NULL by default). It is useful when there are several sets of the same type (e.g. multiple expression assays)
sample.tables	Character with the names of the slots with sample data besides colData.
feature.tables	Character with the names of the slots with feature data besides rowData.
warnings	Logical to indicate if warnings will be displayed.
overwrite	Logical to indicate if the set stored in the slot will be overwritten.

Value

A new MultiDataSet with a slot filled.

Examples

if (require(GenomicRanges) & require(SummarizedExperiment)){
multi <- createMultiDataSet()
counts <- matrix(runif(200 * 6, 1, 1e4), 200)
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], id = LETTERS[1:6])
names(rowRanges) <- 1:200
rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
                            rowRanges=rowRanges, colData=colData)
multi <- add_rse(multi, rse, "rseEx")
}

MultiDataSet documentation built on Jan. 31, 2021, 2:01 a.m.