README.md

Meinter Logo

MeinteR (MEthylation INTERpretation) is an R package that identifies critical differentially methylated sites, based on the following hypothesis: Critical methylation-mediated changes are more likely in genomic regions enriched in cis-acting regulatory elements than in genomic “deserts”. MeinteR calculates the abundance of co-localized elements, such as transcription factor binding sites, tentative splice sites, and other DNA features, such as G-quadruplexes and palindromes that potentially lead to distinct DNA conformational features and rank them with respect to their putative methylation impact.

Package files

Binary Package

Source Package

Package Vignette (PDF)

Package Manual (PDF)

Installation

To install MeinteR and all its dependencies install and load devtools.

Local installation First, download the binary distribution of the package, unzip it to a local folder and run the following commands:

library(devtools)
#Set folder of the package
package.folder <- "~/MeinteR"
install_local(package.folder)

Install from GitHub

MeinteR and its dependencies can be directly installed from GitHub using devtools:

devtools::install_github("andigoni/meinter")

Source code for use cases

Use Case 1: Genome-wide association of G-quadruplexes with DNA methylation using TCGA/GEO breast cancer datasets

Use Case 2: Evaluation of genomic signatures on cancer methylation profiles

Use Case 3: Associating genomic DMS signatures with gene expression

Demo run

library(MeinteR)
rm(list = ls())
#Reorder columns of sample dataset
re.sample <- reorderBed(sample, 1, 2, 3, 5, 4)
#Select sites with delta-beta > 0.50
bed.data <- re.sample[re.sample$score >= 0.50,] 
#Find overlaps with alternative splicing events
altSS <- findAltSplicing(bed.data)
#Find overlaps with splice sites
ss <- findSpliceSites(bed.data, persim = 0.8, offset = 10)
#Find palindromic sequences
pals <- findPals(bed.data)
#Find G-quadruplexes
quads <- findQuads(bed.data, offset = 50)
#Find overlaps with "MA0107.1", "MA0098", "MA115.1", "MA0131.2 transcription factors
tfbs <-
  findTFBS(
    bed.data,
    target = "all",
    tf.ID = c("MA0107.1", "MA0098", "MA115.1", "MA0131.2")
  )
#Find overlaps with conserved transcription factors. ~71MB gzipped file 
#will be downloaded if local path is not set.
ctfbs <- findConservedTFBS(bed.data)
#Find overlaps with DNA shape features
shapes <- findShapes(bed.data)
#Feature weights
weights = list()
weights[["spls"]] = 1
weights[["ctfbs"]] = 1
weights[["tfbs"]] = 1
weights[["pals"]] = 1
weights[["quads"]] = 1
weights[["shapes"]] = 1
#Mapping MeinteR arguments with function outputs
funList = list()
funList[["spls"]] = ss
funList[["altss"]] = altSS
funList[["tfbs"]] = tfbs
funList[["ctfbs"]] = ctfbs
funList[["pals"]] = pals
funList[["quads"]] = quads
funList[["shapes"]] = shapes
#Calculate genomic index
index <- meinter(re.sample, funList, weights)

Citation

A. Malousi et al. "MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment" (submitted)



andigoni/MeinteR documentation built on Aug. 20, 2019, 8:43 a.m.