Entering edit mode
Hi,
I'd like to run snp.plotter - I have two input files to do so: 1) GWAS results and 2) linkage disequilibrium matrix.
#####
1) GWAS results
| chromosome | position | p_value |
| NC_030381.1 | 595 | 6.31E-01 |
| NC_030381.1 | 617 | 2.07E-01 |
| NC_030381.1 | 625 | 9.62E-02 |
2) LD matrix
| SNP1 | SNP2 | SNP3 | |
| SNP1 | 0 | 0.2 | 0.4 |
| SNP2 | 0.2 | 0 | 0.15 |
| SNP3 | 0.15 | 0.4 | 0 |
######
The tutorial of snp.plotter requires genotype file - is there a way to get around it? I have already calculated LD across all snp pairs, so I would like to feed the LD matrix to snp.plotter directly if possible.
Many thanks in advance,
Miyako
