MEDIPS.couplingVector


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


pattern


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


refObj


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.


MEDIPS was developed for analyzing data derived from
methylated DNA immunoprecipitation (MeDIP) experiments followed
by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative
sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others)
including calculation of differential coverage between groups
of samples and saturation and correlation analysis.

Lukas Chavez

MEDIPS

DNA IP-seq data analysis

MEDIPS.couplingVector function

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

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

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.

MEDIPS.couplingVector: Calculates the sequence pattern densities at genome wide windows.

Description

Usage

Arguments

Value

Examples