add_rse {MultiDataSet}R Documentation

Method to add a RangedSummarizedExperiment to MultiDataSet.

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")
}
[Package MultiDataSet version 1.16.0 Index]