Usage
HisCoM-SM is written by R and can be installed by the following steps.
HisCoM-SM can be run by R program. It also needs PLINK, GCTA, and WISARD program. To run the HisCoM-SM, you should first download the ‘Download.zip’ file which contains ‘HisCoM-SM_process.R’ and ‘wisard_1.3.2_win64.zip’.
As inputs, four data files are required: metabolite data fille, SNP data file, pathway-metabolite matching file, and phenotype data file. The following table shows the summary of four files.
Metabolite data (.csv) |
Contains (1) sample ID and (2) metabolite name. |
SNP data (.bed/.bim/.fam) |
SNP BED format data. BED format requires three data files (.bed/.bim/.fam) |
Pathway-metabolite matching file (.set) |
Contains two columns: (1) pathway name and (2) metabolite name. |
Phenotype data file (.csv) |
Contains (1) sample ID, (2) phenotype name, and (3) covariates (age and sex). |
Metabolite data file
First column must be sample id (DIST_ID). This file contains metabolites which will be used in analysis. The other column names are names of metabolites.
Pathway-biomarker matching file
Each line consists of two columns for pathway name and metabolite name, respectively. When reading the matching file, there should be no column names.
Phenotype data file
First column must be sample id (DIST_ID). This file contains phenotype of interest (status) and covariates (AGE, SEX) which will be used in analysis. For phenotype, case = 1, control = 0. For sex, male = 0, female = 1.
The followings are the main output. More detail information about the other output files can be found in http://statgen.snu.ac.kr/wisard/
If there is error, please let us know about the running problem to solve the problem and improve our program.
Contact : tyjung1024@gmail.com