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Post by swvanderlaan on Jul 30, 2018 21:39:41 GMT
Hi,
I'd like to use our eQTL data from monocytes. I ran a genome-wide eQTL analysis using QTLtools and permuted the results. I've read your instructions regarding conversion to BESD-format, but how can I best proceed with output from a permutation run using QTLtools?
Thanks!
Sander
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Post by futaozhang on Aug 19, 2018 11:16:26 GMT
Dear Sander,
Sure, we can do it. If you could provide a sample output of QTLtools, it would accelerate our coding process.
Cheers Futao
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Post by swvanderlaan on Aug 27, 2018 20:53:37 GMT
Dear Futao,
That would be great. See below. If you want I can also send you a complete output?
Thanks!
Sander
ILMN_3239735 01 14362 14362 - 592 -744931 rs60744420:759293:T:A 01 759293 759293 0.0406361 0.0599954 0 ILMN_3239735 01 14362 14362 - 592 -753891 rs2977608 01 768253 768253 0.0148424 -0.0527309 0 ILMN_3239735 01 14362 14362 - 592 -754086 rs12562034 01 768448 768448 0.00911334 0.0817931 0 ILMN_3239735 01 14362 14362 - 592 -755601 rs7518545 01 769963 769963 0.00807449 0.0852071 1 ILMN_3239735 01 14362 14362 - 592 -756524 rs371458725:770886:G:A 01 770886 770886 0.0104909 0.0806576 0 ILMN_3239735 01 14362 14362 - 592 -762870 rs112618790 01 777232 777232 0.021631 0.0776076 0 ILMN_3239735 01 14362 14362 - 592 -767483 rs61768199:781845:A:G 01 781845 781845 0.0495569 0.0573511 0 ILMN_3239735 01 14362 14362 - 592 -777491 rs6684487 01 791853 791853 0.0226044 0.0771181 0 ILMN_3239735 01 14362 14362 - 592 -782764 rs140389426 01 797126 797130 0.0310523 0.0819694 0 ILMN_3239735 01 14362 14362 - 592 -782919 rs76631953 01 797281 797281 0.0336871 0.0813853 0
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Post by futaozhang on Aug 28, 2018 9:16:32 GMT
Dear Sander,
I assume this result was from the nominal run not from a permutation run.
The columns for a nominal run are: 1. The phenotype ID 2. The chromosome ID of the phenotype 3. The start position of the phenotype 4. The end position of the phenotype 5. The strand orientation of the phenotype 6. The total number of variants tested in cis 7. The distance between the phenotype and the tested variant (accounting for strand orientation) 8. The ID of the tested variant 9. The chromosome ID of the variant 10. The start position of the variant 11. The end position of the variant 12. The nominal P-value of association between the variant and the phenotype 13. The corresponding regression slope 14. A binary flag equal to 1 is the variant is the top variant in cis
Did I miss something?
We are coding the functions to transform these QTLtoos formats to BESD format. Would be ready soon.
Cheers Futao
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