How to install PheWeb
To install PheWeb, follow see this GitHub resource.
To import datasets
- Edit pheno-list.json file, include the association files that need to be imported.
- Download the datafiles, make sure the column names are valid.
- Load the association files by running -- pheweb process
Things need to be considered
- When you load your association files, PheWeb will automatically initiate the jobs to download necessary files, make sure you have enough disk space.
- If you have multiple association files, the loading process could take hours.
- If there is a new dataset needs to be added, after adding it into the json file, we will need to ask IT to run pheweb process on genome2.cla.umn.edu.
The file must have colums for:
| column description | name | other allowed column names | allowed values |
|---|---|---|---|
| chromosome | chrom | #chrom, chr | 1-22, X, Y, M, MT, chr1, etc |
| position | pos | beg, begin, bp | integer |
| reference allele | ref | reference | must match reference genome |
| alternate allele | alt | alternate | anything |
| p-value | pval | pvalue, p, p.value | number in [0,1] |
You may also have columns for:
| column description | name | other allowed column names | allowed values |
|---|---|---|---|
| minor allele frequency | maf | number in (0,0.5] | |
| allele frequency | af | a1freq, frq | number in (0,1) |
| AF among cases | case_af | af.cases | number in (0,1) |
| AF among controls | control_af | af.controls | number in (0,1) |
| allele count | ac | integer | |
| effect size | beta | number | |
| standard error of effect size | sebeta | se | number |
| odds ratio | or | number | |
| R2 | r2 | number | |
| number of samples | num_samples | ns, n | integer, must be the same for every variant in its phenotype |
| number of controls | num_controls | ns.ctrl, n_controls | integer, must be the same for every variant in its phenotype |
| number of cases | num_cases | ns.case, n_cases | integer, must be the same for every variant in its phenotype |