Hi,
greetings! I would like to ask a question. I am running coloc for x=a GWAS summary data and y= a mQTL summary data. Now I get error: coloc error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :NA/NaN/Inf in 'x'
In my GWAS sumamry statistics data, there is no NA/NaN/Inf etc. The data is like below. May I ask how to fix this error. Thank you very much for your help in advance.
Lin
GWAS data example:
chr hg37 RS REF ALT beta SE varbeta pvalues MAF N type hg38 snp position
17 3689833 rs8076206 G A 0.0708 0.138 0.019044 0.60899959 0.0001 321047 quant 3786539 3786539 3786539
17 3698280 rs554192590 G T -0.0316 0.155 0.024025 0.839000076 0.0001 321047 quant 3794986 3794986 3794986
17 3698834 rs181797595 C T 0.149 0.156 0.024336 0.338000233 0.0001 321047 quant 3795540 3795540 3795540
17 3702506 rs575324678 G C -0.0652 0.137 0.018769 0.635000402 0.0001 321047 quant 3799212 3799212 3799212
17 3707232 rs919698892 G A 0.0911 0.134 0.017956 0.494999773 0.0001 321047 quant 3803938 3803938 3803938
17 3707266 rs893111380 G C 0.136 0.138 0.019044 0.323999992 0.0001 321047 quant 3803972 3803972 3803972
Hi, greetings! I would like to ask a question. I am running coloc for x=a GWAS summary data and y= a mQTL summary data. Now I get error: coloc error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :NA/NaN/Inf in 'x' In my GWAS sumamry statistics data, there is no NA/NaN/Inf etc. The data is like below. May I ask how to fix this error. Thank you very much for your help in advance. Lin
GWAS data example: chr hg37 RS REF ALT beta SE varbeta pvalues MAF N type hg38 snp position 17 3689833 rs8076206 G A 0.0708 0.138 0.019044 0.60899959 0.0001 321047 quant 3786539 3786539 3786539 17 3698280 rs554192590 G T -0.0316 0.155 0.024025 0.839000076 0.0001 321047 quant 3794986 3794986 3794986 17 3698834 rs181797595 C T 0.149 0.156 0.024336 0.338000233 0.0001 321047 quant 3795540 3795540 3795540 17 3702506 rs575324678 G C -0.0652 0.137 0.018769 0.635000402 0.0001 321047 quant 3799212 3799212 3799212 17 3707232 rs919698892 G A 0.0911 0.134 0.017956 0.494999773 0.0001 321047 quant 3803938 3803938 3803938 17 3707266 rs893111380 G C 0.136 0.138 0.019044 0.323999992 0.0001 321047 quant 3803972 3803972 3803972