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

In js2264/VplotR: Set of tools to make V-plots and compute footprint profiles

A function to compute nucleosome enrichment over a Vmat

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

js2264/VplotR documentation built on Jan. 4, 2024, 7:49 p.m.