Easy workflow for combination of SNP pvalues for gene set from GWAS data. The SNP Z scores are to used to calculate the combinatorial pvalues.
- GWAS file:
A text file with the following information
Chromosome 1
| Markers | Chrom | Position | Pvalue |
|---|---|---|---|
| M1 | 1 | 1 | 0.05 |
| M2 | 1 | 10 | 0.04 |
| M3 | 1 | 25 | 0.01 |
Chromosome 2
| Markers | Chrom | Position | Pvalue |
|---|---|---|---|
| M1 | 2 | 1 | 0.05 |
| M2 | 2 | 10 | 0.04 |
| M3 | 2 | 25 | 0.01 |
The files should be separated based on their chromosome. The chromosome should be named as numbers.
The script to separate chromosome can be found here :
- Genotype file
A genotype text file with MAF numbering with markers in the column and subsequent values in the rows. Each row should represent an accesssion/individual.
| M1 | M2 | M3 | M4 |
|---|---|---|---|
| 0 | 1 | 2 | -9 |
| 0 | 2 | 0 | 1 |
- PCA file
The PCA file that you used to run the generalized linear model. 10 PCAs are preferred.
| PCA1 | PCA2 | PCA3 | PCA4 | PCA5 | PCA6 | PCA7 | PCA8 | PCA9 | PCA10 |
|---|---|---|---|---|---|---|---|---|---|
| 0.07 | 0.78 | 0.08 | 0.65 | 0.48 | 0.84 | 0.15 | 0.26 | 0.47 | 0.15 |
| 0.25 | 0.19 | 0.69 | 0.56 | 0.47 | 0.12 | 0.69 | 0.47 | 0.59 | 0.33 |