Looking to compute R-squared with P-value for LocusZoom plot
0
0
Entering edit mode
5 months ago
skjobs ▴ 190

Looking to compute R-squared values for a list of SNPs associated with specific phenotypes. Interested in having both p-values and R-squared scores for each SNP. Any advice on how to do this efficiently? After Rsqure and the p-value. I want to plot the LocusZoom plot. For the LocusZoom plot input should have p-value of SNPs and R2-Squre. Can anyone advise or help me on how to generate it? I'm working on the plink.

CHROM   POS ID  P   R2
chr1    67216513    rs11576518  8.04E-20    1
chr1    67253446    rs1343151   3.13E-19    0.40487769
chr1    67264372    rs6669582   5.65E-19    0.40081561
chr1    67214307    rs2019262   1.10E-18    0.97752769
chr1    67215986    rs7517847   1.31E-18    0.97851664
chr1    67263180    rs11313807  1.96E-18    0.40462321
chr1    67205233    rs2902440   2.73E-18    0.96000804
R plink LocusZoom GWAS • 411 views
ADD COMMENT
0
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 3063 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6