PTPN22 Reference Data Analysis

Data file: ic_t1d_onengut_allresults.csv.

1. Build 37 method

  • Get corresponding region from immunochip-regions.txt –> chr1:113863087-114527968.
  • Get SNPs in this region from ic_t1d_onengut_allresults.csv file (694 SNPs).
  • Use aligned9.build37.RData to get LD matrix for these SNPs (drop 55 SNPs here which do not appear in this file –> 639 SNPs). Sigma <- ld(Xsub, Xsub, stat="R")
  • Proceed as normal to obtain the 99% credible set, claimed coverage and corrected coverage.
## $Credset
##     name.rs        pp
## 1 rs2476601 0.8640309
## 2 rs6679677 0.1359691
## 
## $Claimed
## [1] 1
## 
## $Corrected
## [1] 0.8035921
## 
## $nSNPs_in_region
## [1] 639