run_me_eQTL: This will run matrixeQTL for eQTL, meQTL and...

In yzeng-lol/meeqtl: The package performs CpG sits methylation dependent eQTL (me_eQTL) analysis

Description

This will run matrixeQTL for eQTL, meQTL and methylation-dependent eQTL

Usage

run_me_eQTL(
  file_edata,
  file_gdata,
  file_mdata,
  file_tss_loci,
  file_snp_loci,
  file_cpg_loci,
  geneSnpMaxDistance = 5e+05,
  cpgSnpMaxDistance = 5e+05,
  cluster_core = 2
)

Arguments

file_edata	path to edata file
file_gdata	path to gdata file
file_mdata	path to mdata file
file_tss_loci	path to TSS bed file
file_snp_loci	path to SNP bed file
file_cpg_loci	path to CpG bed file
geneSnpMaxDistance	max distance between snp and gene, default 500000
cpgSnpMaxDistance	max distance between snp and probe, default 500000
cluster_core	doParallel core, default 2 for local
x	eqtl dataframe, e.g., res$gene

yzeng-lol/meeqtl documentation built on Dec. 23, 2021, 9:10 p.m.