Here's a breakdown of my situation. I'm trying to pass to pass the following command options in Plink:
--dosage MY_DATA.dosage
--fam MY_DATA.fam
--clump GWASresults.assoc
--clump-p1 1
--clump-p2 1
--clump-r2 0.1
--clump-kb 500
--out MY_DATA_CLUMPED
Strangely, this returns an association summary file. It's as though Plink is ignoring these prompts to clump, and proceeds with a default track of testing for allele association to the phenotype. I expected this to turnover a file type similar to that presented in an example from the Plink website:
CHR F SNP BP P TOTAL NSIG S05 S01 S001 S0001 SP2
8 1 rs1234564 15716326 5.01e-07 0 0 0 0 0 0 NONE
14 1 rs1205236 69831825 1.46e-06 0 0 0 0 0 0 NONE
2 1 rs16331058 114547107 2.33e-06 3 0 0 0 0 3 rs2366902(1),...
2 1 rs759966 54902416 9.28e-06 4 0 0 0 3 1 rs12538389(1),...
11 1 rs8031586 44633498 9.75e-06 1 0 0 0 0 1 rs802328(1)
12 1 rs12431413 30028246 9.89e-06 0 0 0 0 0 0 NONE
6 1 rs14966070 62091121 1.07e-05 0 0 0 0 0 0 NONE
For reference, MY_DATA
(--dosage
file) is formatted as shown in this example:
SNP A1 A2 F1 I1 F2 I2 F3 I3
rs0001 A C 0.98 0.02 1.00 0.00 0.00 0.01
rs0002 G A 0.00 1.00 0.00 0.00 0.99 0.01
Has anyone successfully "clumped" dosage data? If so, what commands should I be passing to get the expected output?
Thanks for considering my question!
Bummer! And do you know off hand of a program that converts the style of .dosage files I'm working with to say .ped? The
--make-bed
option doesn't produce anything valid :(I'm not aware of one, though it shouldn't be too difficult to write a script for this. PLINK 1.9 is only capable of performing this conversion for Oxford .gen files.
Thanks for bringing clarity to this!