hmagmaR - Incorporation of chromatin interaction and epigenetic profiles to predict risk genes: Gene Level Analysis using MAGMA (HMAGMA) How to Install: 1. `remotes::install_github("aydanasg/hmagmaR")` 2. Required packages: data.table (>= 1.14.8), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), org.Hs.eg.db (>= 3.18.0), GenomicRanges (>= 1.54.1), ChIPseeker (>= 1.38.0), dplyr (>= 1.1.3) 3. Note that, to run `GeneLevelAnalysis_hmagma()` function you need to install a correct version of magma from here: https://cncr.nl/research/magma/ Example: 1. Generating annotation file using `AnnotationFileHmagma()` function to be used in `GeneLevelAnalysis_hmagma()` function `hmagmaR::AnnotationFileHmagma(fileName = {fileName}, hic = {hic}, regulatoryRegions = {regulatoryRegions}, snps = {snps}, annotated_genes = {annotated_genes}, snpgeneexon = {snpgeneexon}, AnnotationFile.path = "/.../annotation_output/")` annotated_genes and snpgeneexon files can be taked from data/ folder where data is generated using TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db and 1,000 Genomes reference data files (.bin) from European population 2. Running gene level analysis using `GeneLevelAnalysis_hmagma()` function `hmagmaR::GeneLevelAnalysis_hmagma(magma="/.../magma", g1000="/.../g1000_eur", gwas="/.../{gwas_summary}.tsv", AnnotationFile="/.../{fileName}.transcript.annot", #output of `AnnotationFileHmagma()` function output="/.../hmagma_output/{fileName}")`