Extracts Gene Subsets from a SummarizedExperiment object

splitByGeneSet(se, genesets)

Arguments

se	A SummarizedExperiment object.
genesets	A list of gene sets.

Value

A list of SummarizedExperiment objects.

Examples

# Prepare example data ----

sample_names <- c("A", "B")

se_list <- generateDeeptoolsExperiments(20, 10, sample_names)
se_list
#> $A
#> class: RangedSummarizedExperiment 
#> dim: 20 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(20): GR_1 GR_2 ... GR_19 GR_20
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):
#> 
#> $B
#> class: RangedSummarizedExperiment 
#> dim: 20 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(20): GR_1 GR_2 ... GR_19 GR_20
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):
#> 

# Usage ----

range_sets <- list(set1=c("GR_1"), set2=c("GR_2", "GR_3"))
splitByGeneSet(se_list[[1]], range_sets)
#> $set1
#> class: RangedSummarizedExperiment 
#> dim: 1 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(1): GR_1
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):
#> 
#> $set2
#> class: RangedSummarizedExperiment 
#> dim: 2 10 
#> metadata(0):
#> assays(1): matrix
#> rownames(2): GR_2 GR_3
#> rowData names(0):
#> colnames(10): 1 2 ... 9 10
#> colData names(0):
#>