meinter: Calculate the genomic index of methylation sites based on the...

In andigoni/MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

Description

Calculates the genomic index given a set of features pre-analysed using MeinteR's 'find*' functions. First, the function builds the local genomic signature of each site and the it calculates the genomic index using a weighting scheme.

Usage

meinter(bed.data, funList, weights)

Arguments

bed.data	A data frame containing input bed-formatted data
funList	List of 'find*' functions outputs. At least one core function is needed to calculate the genomic index. Valid element names of the list: 'spls'-'findSpliceSites', 'altss'-'findAltSplicing', 'ctfbs'-'findConservedTFBS', 'tfbs'-'findTFBS', 'pals'-'findPals', 'quads'-'findQuads', 'shapes'-'findShapes'
weights	A list of positive values corresponding to feature weights [0,10]. Same list elements with 'funList' list

Value

A data frame with the genomic index of the input data

andigoni/MeinteR documentation built on Oct. 1, 2021, 9:33 p.m.