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13 months ago
skjobs
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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
It's all in the manuals: