MEDIPS.couplingVector {MEDIPS}R Documentation

Calculates the sequence pattern densities at genome wide windows.

Description

The function calculates the local densities of a defined sequence pattern (e.g. CpGs) and returns a COUPLING SET object which is necessary for normalizing MeDIP data.

Usage

MEDIPS.couplingVector(pattern="CG", refObj=NULL)

Arguments

pattern

defines the sequence pattern, e.g. CG for CpGs.

refObj

a MEDIPS Set or MEDIPS ROI Set that serves as reference for the genome and window parameters.

Value

A COUPLING SET object.

Author(s)

Lukas Chavez

Examples


library("MEDIPSData")
library("BSgenome.Hsapiens.UCSC.hg19")

data(hESCs_MeDIP)
CS = MEDIPS.couplingVector(pattern="CG", refObj=hESCs_MeDIP)


[Package MEDIPS version 1.36.0 Index]