## 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
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