nucleosomeEnrichment.Vmat: A function to compute nucleosome enrichment over a Vmat

In VplotR: Set of tools to make V-plots and compute footprint profiles

Description

A function to compute nucleosome enrichment over a Vmat

Usage

## S3 method for class 'Vmat'
nucleosomeEnrichment(x, background, plus1_nuc_only = FALSE, ...)

Arguments

x	a computed Vmat. Should be un-normalized.
background	a background Vmat. Should be un-normalized.
plus1_nuc_only	Boolean, should compute nucleosome enrichment only for +1 nucleosome?
...	additional parameters

Value

list

Examples

data(bam_test)
data(ce11_proms)
V <- plotVmat(
    bam_test,
    ce11_proms,
    normFun = '',
    return_Vmat = TRUE
)
V_bg <- plotVmat(
    bam_test,
    sampleGRanges(ce11_proms),
    normFun = '',
    return_Vmat = TRUE
)
n <- nucleosomeEnrichment(V, V_bg)
n$fisher_test
n$plot

VplotR documentation built on Nov. 8, 2020, 7:50 p.m.