giupardeb/epimethex

EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between methylation and gene expression data.

EpiMethEx (Epigenetic Methylation and Expression)

The EpiMethEx package is under submission on bioconductor (https://github.com/Bioconductor/Contributions/issues), to use it you can follow the instructions below.

HOW-TO execute the script

1. clone the repository
2. execute R CMD build EpiMethEx
3. install package into R: install.packages(path_to_file, repos = NULL, type="source")
4. create three datasets as in the example. The example below is a extract of the datasets TCGA-SKCM (https://xenabrowser.net/datapages/?cohort=TCGA%20Melanoma%20(SKCM)):

 Annotations <- data.frame(
 ID = c("cg11663302","cg01552731", "cg09081385"),
 Relation_to_UCSC_CpG_Island = c("Island","N_Shore","N_Shore"),
 UCSC_CpG_Islands_Name = c("chr1:18023481-18023792","chr19:46806998-46807617",
 "chr12:120972167-120972447"),
 UCSC_RefGene_Accession = c("NM_001011722","NM_152794","NM_014868"),
 Chromosome_36 = c("1","19","12"),
 Coordinate_36 = c("17896255","51498747","119456453"),
 UCSC_RefGene_Name = c("ARHGEF10L","HIF3A","RNF10"),
 UCSC_RefGene_Group =c("Body","1stExon","TSS200"),
 stringsAsFactors=FALSE)

 Expressions <- data.frame(
 'sample' = c("ARHGEF10L", "HIF3A", "RNF10"),
 'TCGA-YD-A89C-06' = c(-0.746592469762, -0.753826336325, 0.4953280),
 'TCGA-Z2-AA3V-06' = c(0.578807530238, -2.30662633632, 0.1023280),
 'TCGA-EB-A3Y6-01' = c(-0.363492469762, -2.67922633632, -0.6147720),
 'TCGA-EE-A3JA-06' = c(-2.97279246976, -3.61932633632, 0.02932801),
 'TCGA-D9-A4Z2-01' = c(-0.128492469762, 0.679073663675, 0.4017280),
 'TCGA-D3-A51G-06' = c(-0.4299925, -4.0626263, -1.0136720),
 stringsAsFactors=FALSE)

 Methylation <- data.frame(
 'sample' = c("cg11663302", "cg01552731", "cg09081385"),
 'TCGA-YD-A89C-06' = c(0.9856, 0.7681, 0.0407),
 'TCGA-Z2-AA3V-06' = c(0.9863, 0.8551, 0.0244),
 'TCGA-EB-A3Y6-01' = c(0.9876, 0.6473, 0.028),
 'TCGA-EE-A3JA-06' = c(0.9826, 0.4587, 0.0343),
 'TCGA-D9-A4Z2-01' = c(0.9881, 0.8509, 0.0215),
 'TCGA-D3-A51G-06' = c(0.9774, 0.813, 0.0332),
 stringsAsFactors=FALSE)

4.1 or use the "curatedTCGAData" package:

source("https://bioconductor.org/biocLite.R")
BiocInstaller::biocLite("curatedTCGAData")
library(curatedTCGAData)
library(MultiAssayExperiment)

Methylation <- curatedTCGAData(diseaseCode = "SKCM", assays = "Methylation", dry.run = F)
Expressions <- curatedTCGAData(diseaseCode = "SKCM", assays = "RNASeq2GeneNorm", dry.run = F)

it's most important to remember that curatedTCGAData doesn't allow to download dataset of Annotations,therefore it must be loaded manually through csv file or created ad hoc

4.2 or use the csv file:

Expression <- read.csv2("Expressions.csv", header = T,sep = ";",stringsAsFactors=FALSE)
Annotations <- read.csv2("Annotations.csv",header = T,sep = ";",stringsAsFactors=FALSE)
Methylation <- read.csv2("Methylation.csv",header = T,sep = ";",stringsAsFactors=FALSE)

5. Execute the following istruction:

library(EpiMethEx)
epimethex.analysis(Expressions, Annotations, Methylation, 1, 3, 2,TRUE, TRUE, FALSE)

Parameters

1. first parameter is a genes expression of data
2. Second parameter is Annotations of data
3. Third parameter is Methylation of data
4. Fourth parameter and fifth parameter are the range of genes to consider
5. sixth parameter, is the number of cores that you can use to analysis
6. seventh parameter determines if genes expression of data are linear
7. eighth parameter determines the test to apply on expression dataset. If TRUE will apply t-student test, otherwise will apply Kolmogorov-Smirnov test
8. ninth parameter, determines the test to apply on methylation dataset. If TRUE will apply t-student test, otherwise will apply Kolmogorov-Smirnov test

HOW TO FILTER

To further evaluate the biological significance of the methylation hotspots involved in gene regulation mechanisms, is possible to filter EpiMethEx output with an additional R script (https://github.com/giupardeb/EpiMethEx-Filter)

TESTING (System Configuration)

• OS: Ubuntu 18.04 - 64 bit
• CPU: 8 Cores
• RAM: 32GB
• R: v3.4.4
• MAX range of genes: 1000

epimethex's Issues

Installation failed

Hi I'm trying to install this, running: R CMD build EpiMethEx. I have R version 4.1, running on mac (x86_64-apple-darwin17.0 ) and BiocManager v 1.30.16. FYI It failed multiple times and requires the following to be installed (and possibly other packages that I already had installed):

BiocManager::install("MultiAssayExperiment")
install.packages("miscTools")
install.packages("RcmdrMisc")
install.packages("psych")

Would recommend adding required installs to your package so users don't have to install them i.e. at the top of the script:

packages <- c("miscTools", "RcmdrMisc", "psych")
install.packages(setdiff(packages, rownames(installed.packages())))

Anyway following installing the required packages I got the error:

* checking for file ‘EpiMethEx/DESCRIPTION’ ... OK
* preparing ‘EpiMethEx’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epimethex_analysis.Rmd’ using rmarkdown
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in xtfrm.data.frame(x) : cannot xtfrm data frames
Warning in `[<-.factor`(`*tmp*`, ri, value = -1.859692469761) :
  invalid factor level, NA generated
Warning in `[<-.factor`(`*tmp*`, ri, value = -0.396742484881) :
  invalid factor level, NA generated
Warning in `[<-.factor`(`*tmp*`, ri, value = 0.225157530238) :
  invalid factor level, NA generated
Quitting from lines 44-80 (epimethex_analysis.Rmd)
Error: processing vignette 'epimethex_analysis.Rmd' failed with diagnostics:
task 1 failed - "undefined columns selected"
--- failed re-building ‘epimethex_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘epimethex_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted

Do you have a pre-built version I can install? Otherwise please let me know if you update the code with the error resolved or if this is no longer under development, cheers!