# If you use this code to analyze data, please cite the following paper:
# Lin W-Y, Huang C-C, Liu Y-L, Tsai S-J, Kuo P-H (2019). Genome-wide gene-environment interaction analysis with set-based association tests. Frontiers in Genetics, 9, Article 715 (15 pages).
# Any questions or comments, please contact: Wan-Yu Lin, linwy@ntu.edu.tw, Institute of Epidemiology and Preventive Medicine, National Taiwan University College of Public Health
# Thank you.
##########################################################################################
Suppose we have "merge16555.bim", "merge16555.bed", and "merge16555.fam". If the phenotypes and covariates are put in "phenotype_and_covariate".
Step 1, to generate the map file for each chromosome. From the following commands, we can obtain "chr1.map", ..., "chr22.map".
plink --bfile merge16555 --recode --chr 1 --out chr1 --noweb
plink --bfile merge16555 --recode --chr 2 --out chr2 --noweb
.........
plink --bfile merge16555 --recode --chr 22 --out chr22 --noweb
Step 2, to recode the genotypes into 0, 1, 2. From the following commands, we can obtain "myRdata1.raw", ..., "myRdata22.raw".
plink --bfile merge16555 --recodeA --chr 1 --out myRdata1 --noweb
plink --bfile merge16555 --recodeA --chr 2 --out myRdata2 --noweb
.........
plink --bfile merge16555 --recodeA --chr 22 --out myRdata22 --noweb
Genelist (the human genome GRCh37/hg19 assembly ±50 kb flanking regions of a gene) [genelist.csv]
The R code to perform the ADABF analysis for a whole chromosome [Genome_wide_ADABFGE.R]
The Perl script to concatenate the above actions, analyzing from chromosome 1, 2, ..., to 22 [Genome_wide_ADABFGE.pl]
Please put these files in a directory, and run the perl command "nohup perl ./Genome_wide_ADABFGE.pl &"
Then you will see the result like this:
Column 1: chromosome
Column 2: starting base pair for the gene analysis, based on the human genome GRCh37/hg19 assembly -50 kb
Column 3: ending base pair for the gene analysis, based on the human genome GRCh37/hg19 assembly +50 kb
Column 4: the ADABF P-value for GxE analysis
Thanks for your interest.
Return to the ADABF GxE method webpage
Return to Wan-Yu Lin's homepage