Hi all,
I have the following plinkseq output. Can anyone help me in understanding it. Also considering its a case control study of 1000 sample each which test should I use.
NVAR TEST P I DESC
19 BURDEN 0.375 0.0434783 231/224
27 BURDEN 0.0440678 0.00340136 81/62
9 BURDEN 1 0.2 38/46
26 BURDEN 0.714286 0.166667 799/824
10 BURDEN 0.714286 0.166667 15/16
2 BURDEN 0.5 0.2 1/1
6 BURDEN 0.833333 0.2 2/4
26 BURDEN 0.102362 0.00793651 79/66
7 BURDEN 1 0.2 604/663
9 BURDEN 0.428571 0.05 533/542
14 BURDEN 0.00953029 0.000681199 12/3
5 BURDEN 0.538462 0.333333 5/4
36 BURDEN 0.000788777 5.63444e-05 706/615
1 BURDEN 0.833333 0.2 378/381
2 answers
You need to read the manual for the software to know what it makes. If you don't understand the procedure, then chances are your input data is malformed too, and the results will be wrong.
From the output I'd guess it has performed "BURDEN" tests over NVAR snp segments and reported a p<0.01 hit over 14 snps, with 12 cases and 3 controls sharing the sequence.
The Plinkseq documentation page for association tests shows your BURDEN table with columns of genomic locations.
They explain that the I column represents the diversity at the locus, high values indicating less unique sequence observations. Therefore your low P and low I regions are good candidates for something occurring more often in cases than controls.
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karl.stamm
I'm not sure what the DESC column is. Subject totals was a guess. It doesn't really make sense to have a P=1.0 when 313 cases and 147 controls carry the a 64 SNP haplotype.
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karl.stamm
From the output LOCUS, POS, ALIAS columns are missing.
Interpretation, it is a pseq burden (Excess of rare alleles in cases compared to controls) result output for 14 loci each having NVAR number of SNPs. e.g.: the first line, on that locus there are 19 SNPs grouped together for burden.
"The P field is based on permutation, the empirical significance. The I field indicates the proportion of null replicates for which the best test statistic was tied. ... The DESC field contains the number of case/control minor alleles." - pseq gene-based tests
pseq 0.09 version includes SKAT test as well.
Dear Tokhir,
Thanks for your answer. If you don't mind can you please do let me know when I should use calpha or burden test for case control study. I am new to human genetics as well as bio-stats; so trying to gain idea about this.
Also I did not get this "pseq 0.09 version includes SKAT test as well" in the pseq note.
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