A function to compute nucleosome enrichment over a set of GRanges

# S3 method for GRanges
nucleosomeEnrichment(x, granges, plus1_nuc_only = FALSE, verbose = TRUE, ...)

Arguments

x: GRanges, paired-end fragments
granges: GRanges, loci to map the fragments onto
plus1_nuc_only: Boolean, should compute nucleosome enrichment only for +1 nucleosome?
verbose: Boolean
...: additional parameters

Value

list

Examples

data(bam_test)
data(ce11_proms)
n <- nucleosomeEnrichment(bam_test, ce11_proms)
#> Computing Vmat...
#> Computing background...
#> Computing enrichment...
n$fisher_test
#> 
#> 	Fisher's Exact Test for Count Data
#> 
#> data:  matrix(vec, ncol = 2)
#> p-value = 0.8227
#> alternative hypothesis: true odds ratio is not equal to 1
#> 95 percent confidence interval:
#>  0.4141458 3.0139383
#> sample estimates:
#> odds ratio 
#>   1.133024 
#> 
n$plot