add_rse {MultiDataSet} | R Documentation |
RangedSummarizedExperiment
to MultiDataSet
.This method adds or overwrites a slot of a MultiDataSet
with the content
of the given RangedSummarizedExperiment
.
add_rse(object, set, dataset.type, dataset.name = NULL, sample.tables = NULL, feature.tables = NULL, warnings = TRUE, overwrite = FALSE)
object |
|
set |
Object derived from |
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. |
A new MultiDataSet
with a slot filled.
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") }