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}")`