A function to compute nucleosome enrichment over a set of GRanges

A function to compute nucleosome enrichment over a set of GRanges

# S3 method for GRanges
nucleosomeEnrichment(bam_granges, granges,
  normalize = TRUE, Vmt2 = NULL, estimate_background = TRUE,
  plus1_nuc_only = FALSE, verbose = TRUE, genome = "ce11",
  roll = 1, normFun = "pctsum", ...)

Arguments

bam_granges

GRanges. The paired-end fragments
granges

GRanges. The regions to map the fragments onto
estimate_background

Boolean Should the background be estimated automatically?
plus1_nuc_only

Should compute nucleosome enrichment only for +1 nucleosome?
verbose

Boolean
genome

a BSgenome object. See getChromSizes for more details

Value

list