Sib-pair Command: schaid

Class	Analysis and data manipulation command
Name	schaid
Arguments	<binary trait> <marker> [<allele>]

Performs the Schaid and Sommer [1993] genotypic risk ratio test for familial association under the assumption of Hardy-Weinberg equilibrium, as well as the "Conditional on Parental Genotypes" version that is equivalent to the genotypic TDT. Only one allele (defaulting to the commonest) is tested versus all others, and two penetrance ratios (GRR₂=f₂/f₀ and GRR₁=f₁/f₀) are estimated, along with the LR chi-square test that GRR₂=GRR₁=1.

Example:

>> schaid  blue rs11855019

--------------------------------------------------
Schaid & Sommer analysis of trait "blue"
--------------------------------------------------
Versus allele T   of marker rs11855019

------------------------------------------------------------
      Mating         Total Expected   T/T     T/C     C/C
------------------------------------------------------------
  T/T   x   T/T        462    471.9   462       x       x
  T/T   x   T/C        204    185.1   147      57       x
  T/T   x   C/C          3      9.1     x       3       x
  T/C   x   T/C         16     18.1     9       5       2
  T/C   x   C/C          1      1.8     x       1       0
  C/C   x   C/C          0      0.2     x       x       0
------------------------------------------------------------

Freq of T   allele   =     0.872
N affected children  =   686

HWE Chi-square (2 df)=    50.93 (P=0.000)
Genotypic RR1 (f1)   =     2.41 (95%CI=    0.59 to     9.94)
Genotypic RR2 (f2)   =     6.60 (95%CI=    1.59 to    27.43)
Attributable risk    =     0.82

CPG Chi-sq    (2 df) =    48.34 (P=0.000)
Genotypic RR1 (f1)   =     1.87 (95%CI=    0.42 to     8.46)
Genotypic RR2 (f2)   =     4.94 (95%CI=    1.09 to    22.26)
Attributable risk    =     0.76