# _ewas files are associations between CGmet levels and traits. 
# _ewas.hypervariableCG are EWAS associations to hypervariable CpGs only.
# Hypervariable_CG file has the chr,bp locations (mm9) of Hypervariable CpGs
# Clinical trait and Metabolite EWAS associations have gene annotations, which correspond to any genes found within 10Mb of the association. Each association at p< 1e-05 is also present in the file by itself without gene annotations.
# File "Liver_CGmet.gwas" has results for GWAS between DNA methylation (traits) and SNPs. Associations are all p<1e-06.
# Chromosome and base-pair positions correspond mm9.
# Chromosomes X, Y, MT are coded as 20,21,22.
# Headers for each file are described below:

# Headers for "Clinical_traits_ewas" and "Metabolites_ewas"
# 1) Pval
# 2) Beta
# 3) Phenotype
# 4) Phenotype class (Clinical trait or metabolite)
# 5-8) are CG annotations
# 5) CG annotation chr,
# 6) CG annotation bp
# 7) CG annotation genome-wide bp position
# 8) CG index
# 9)  Distance (in bp) between gene start and methylation site (gene - CG)
# 10) Distance (in bp) between gene end and methylation site (gene - CG)
# 11) Intra-genic (1) or intergenic (0)
# 12-19) are Gene annotations
# 12) Gene index
# 13) Gene annotation chr
# 14) Gene annotation bp_start
# 15) Gene annotation bp_end
# 16) Gene annotation genome-wide start bp position
# 17) Gene annotation genome-wide end bp position 
# 18) Gene annotation geneID (transcriptID from GTF)
# 19) Gene annotation genesymbol

# Headers for "Liver_expression_ewas"
# 1) Pval
# 2) Beta
# 3) Distance (in bp) between gene start and methylation site (gene - CG)
# 4) Distance (in bp) between gene end and methylation site (gene - CG)
# 5) Association intra-genic or inter-genic (1/0)?
# 6-9) are CG annotations
# 6) CG annotation chr,
# 7) CG annotation bp
# 8) CG annotation genome-wide bp position
# 9) CG index
# 10-16) are Gene annotations
# 10)  Gene index
# 11) Gene annotation chr
# 12) Gene annotation bp_start
# 13) Gene annotation bp_end
# 14) Gene annotation genome-wide start bp position
# 15) Gene annotation genome-wide end bp position 
# 16) Gene annotation gene ProbeID
# 17) Gene annotation genesymbol 

# Headers for "Liver_proteomics_ewas"
# 1) Pval
# 2) Beta
# 3) Distance (in bp) between gene start and methylation site (gene - CG)
# 4) Distance (in bp) between gene end and methylation site (gene - CG)
# 5) Association intra-genic or inter-genic (1/0)?
# 6-9) are CG annotations
# 6) CG annotation chr,
# 7) CG annotation bp
# 8) CG annotation genome-wide bp position
# 9) CG index
# 10-16) are Gene annotations
# 10) Gene index
# 11) Gene annotation chr
# 12) Gene annotation bp_start
# 13) Gene annotation bp_end
# 14) Gene annotation genome-wide start bp position
# 15) Gene annotation genome-wide end bp position 
# 16) Gene annotation Entrez geneID
# 17) Gene annotation geneSymbol 

# Headers for "Liver_CGmet.gwas"
# 1)  Pval
# 2)  Distance (in bp) between SNP and methylation site
# 3-6) are CG annotations
# 3)  CG annotation chr,
# 4)  CG annotation bp
# 5)  CG annotation genome-wide bp position
# 6)  CG index
# 7-11) are SNP annotations
# 7)  SNP annotation chr,
# 8)  SNP annotation bp
# 9)  SNP annotation genome-wide bp position
# 10) SNP index
# 11) SNP rsID