chr1swallace
commented
2 years ago can you tell me what your input looks like, how you are calling coloc.abf (which arguments are you giving it)?
From: marielohcs @.> Sent: 20 July 2022 18:24 To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] Output returns NaN (Issue #97)
I ran the coloc.abf as usual, but had the results returning as NaN.
This is what I get, including first 5 lines of $results
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf NaN NaN NaN NaN NaN [1] "PP abf for shared variant: NaN%" $summary nsnps PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf 6383 NaN NaN NaN NaN NaN
$results snp V.df1 z.df1 r.df1 lABF.df1 V.df2 z.df2 r.df2 lABF.df2 internal.sum.lABF SNP.PP.H4 1 33188495 0.00004489 -0.089552239 0.9988790 -3.392765344 1.600e-07 0.75000000 0.9855609 -1.841718e+00 -5.234484e+00 NaN 2 33188863 0.00466489 0.975109810 0.8955580 -0.703795936 1.690e-06 -1.38461538 0.8659902 -1.748003e-01 -8.785963e-01 NaN 3 33189873 0.00007569 1.011494253 0.9981113 -2.625345432 2.500e-07 -2.00000000 0.9776207 5.543286e-02 -2.569913e+00 NaN 4 33191495 0.00006561 3.481481481 0.9983624 2.843159673 8.100e-07 1.44444444 0.9309523 -3.653000e-01 2.477860e+00 NaN 5 33191784 0.00002916 -1.518518519 0.9992715 -2.460173422 1.600e-07 0.00000000 0.9855609 -2.118907e+00 -4.579081e+00 NaN
I am not sure what is wrong, but am wondering if it is because my p-values for 1 of the datasets can get quite small? (it can go down to E-75 or so; it is a QTL dataset)
Looking for your kind advice please; Thanks!
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I ran the coloc.abf as usual, but had the results returning as NaN.
This is what I get, including first 5 lines of $results
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf NaN NaN NaN NaN NaN [1] "PP abf for shared variant: NaN%" $summary nsnps PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf 6383 NaN NaN NaN NaN NaN
$results snp V.df1 z.df1 r.df1 lABF.df1 V.df2 z.df2 r.df2 lABF.df2 internal.sum.lABF SNP.PP.H4 1 33188495 0.00004489 -0.089552239 0.9988790 -3.392765344 1.600e-07 0.75000000 0.9855609 -1.841718e+00 -5.234484e+00 NaN 2 33188863 0.00466489 0.975109810 0.8955580 -0.703795936 1.690e-06 -1.38461538 0.8659902 -1.748003e-01 -8.785963e-01 NaN 3 33189873 0.00007569 1.011494253 0.9981113 -2.625345432 2.500e-07 -2.00000000 0.9776207 5.543286e-02 -2.569913e+00 NaN 4 33191495 0.00006561 3.481481481 0.9983624 2.843159673 8.100e-07 1.44444444 0.9309523 -3.653000e-01 2.477860e+00 NaN 5 33191784 0.00002916 -1.518518519 0.9992715 -2.460173422 1.600e-07 0.00000000 0.9855609 -2.118907e+00 -4.579081e+00 NaN
I am not sure what is wrong, but am wondering if it is because my p-values for 1 of the datasets can get quite small? (it can go down to E-75 or so but not 0; it is a QTL dataset)
If that is indeed the case, is there any solution, or will you suggest I artificially inflate my p-values (i.e. multiply a constant throughout)? Looking for your kind advice please; Thanks!