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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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SKAT p-value show "-nan" in gene-based association #102

Open suraj86nong opened 4 years ago

suraj86nong commented 4 years ago

Hi, I had encountered a problem of "-nan" in pvalue while running the SKAT for gene-based association. For the same gene, the burden test and single variant analysis were properly run. SKATO gave "NA" result. Here, I have given an example. Kindly help me to understand and solve this problem. Thank you.

SKAT result

Range RANGE N_INFORMATIVE NumVar NumPolyVar Q Pvalue NumPerm ActualPerm Stat NumGreater NumEqual PermPvalue TMEM67 8:93758521-93793294 2992 6 3 0 -nan 10000 1000 0 0 1000 0.5

SKATO result

Range RANGE N_INFORMATIVE NumVar NumPolyVar Q rho Pvalue TMEM67 8:93758521-93793294 2992 6 3 NA NA NA

Burden result

Range RANGE N_INFORMATIVE NumVar NumPolyVar NonRefSite Pvalue TMEM67 8:93758521-93793294 2992 6 3 6 0.718514

Single variant result

CHROM POS REF ALT N_INFORMATIVE AF INFORMATIVE_ALT_AC CALL_RATE HWE_PVALUE N_REF N_HET N_ALT U_STAT SQRT_V_STAT ALT_EFFSIZE PVALUE 8 93765617 A T 2992 0.000501337 3 1 1 2989 3 0 5.75725 1.73618 1.90997 0.000913009 8 93765648 T G 2992 0.000335121 2.00536 1 1 2990 2 0 -4.37543 1.41782 -2.1766 0.00202849 8 93793294 C T 2992 0.000167112 1 1 1 2991 1 0 -0.688028 1.00272 -0.684302 0.492611