Hi,
I have PRSet pathway-analysis outputs for three phenotypes: seropositive RA, seronegative RA, and PMR. I would like to perform a SNP-level comparison within each pathway.
Specifically, can we:
extract the SNPs contributing to each PRSet pathway,
obtain or re-estimate phenotype-specific SNP beta and SE values for each phenotype in each Significant pathway based on competitive p-value,
compare the same SNP effects across SP-RA, SN-RA, and PMR using Z-score/heterogeneity tests?
Since the SNP P values in the PRSet .snp files come from the same base GWAS, I am particularly interested in estimating phenotype-specific SNP effects from the target genotype/phenotype data rather than comparing the PRSet base-GWAS P values directly.
Any Help is highly appreciated.
Best wishes,
Abhishek
Hi,
I have PRSet pathway-analysis outputs for three phenotypes: seropositive RA, seronegative RA, and PMR. I would like to perform a SNP-level comparison within each pathway.
Specifically, can we:
extract the SNPs contributing to each PRSet pathway,
obtain or re-estimate phenotype-specific SNP beta and SE values for each phenotype in each Significant pathway based on competitive p-value,
compare the same SNP effects across SP-RA, SN-RA, and PMR using Z-score/heterogeneity tests?
Since the SNP P values in the PRSet .snp files come from the same base GWAS, I am particularly interested in estimating phenotype-specific SNP effects from the target genotype/phenotype data rather than comparing the PRSet base-GWAS P values directly.
Any Help is highly appreciated.
Best wishes,
Abhishek