Power analysis with powsimR can be done in the following steps:

1. Set up a loading function:

get_annotated_regions_from_gff <- function(file_name) { 
    gff <- rtracklayer::import.gff(file_name) 
    as(gff, "GRanges") 
}

2. Get counts in windows across the whole genome:

whole_genome <- csaw::windowCounts( 
    file.path(getwd(), "datasets", "ch1", "windows.bam"),
    bin = TRUE,
    filter = 0,
    width = 500,
    param = csaw::readParam(
        minq = 20,
        dedup = TRUE,
        pe = "both"
    )
)
colnames(whole_genome) <- c("small_data")

annotated_regions <- get_annotated_regions_from_gff(file.path(getwd(), "datasets", "ch1", "genes.gff"))

3. Find overlaps between annotations and our windows, and subset the windows:

library(IRanges)
library(SummarizedExperiment)
windows_in_genes <-IRanges::overlapsAny( SummarizedExperiment::rowRanges(whole_genome), annotated_regions ) 

4. Subset the windows into those in annotated and non-annotated regions:

annotated_window_counts <- whole_genome[windows_in_genes,] 
non_annotated_window_counts <- whole_genome[ ! windows_in_genes,] 

5. Get the data out to a count matrix:

assay(non_annotated_window_counts)