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