Sib-pair Command: sdt

Class	Analysis and data manipulation command
Name	sdt
Arguments	<binary trait> [ped|stratum <stratum_indicator>]

Prints sibship-matched case-control conditional logistic regression results for all marker loci versus a binary trait, where sibships contain affected and unaffected individuals at that trait. The addition of the ped keyword gives an analysis stratified on pedigree, while a categories of a specified variable are used if the stratum keyword is used.

Increasing the print level results in a list of strata, IDs and covariate values.

Example:

>> include liuex.in
>> sdt AD
------------------------------------------------
SDT for trait "ad" v. all markers
------------------------------------------------


Marker         Typed  Allels Chi-square Asy-P  ST-P
-------------- ------ ------ ---------- ------ ------
apoe               75      3       11.5 0.0032 0.0044 SDT   *


>> set plevel 2
>> sdt AD

------------------------------------------------
SDT for trait "ad" v. all markers
------------------------------------------------

SDT: "apoe"
----------------
Stratum     1 Case          F102--203 2. 0.
Stratum     1 Control       F102--202 2. 0.
Stratum     2 Case          F102--305 1. 1.
Stratum     2 Control       F102--303 2. 0.
Stratum     2 Control       F102--307 1. 1.
[...]
Stratum    16 Case          F205--301 1. 1.
Stratum    16 Case          F205--303 1. 1.
Stratum    16 Case          F205--304 1. 1.
Stratum    16 Case          F205--308 1. 1.
Stratum    16 Control       F205--306 1. 1.
Stratum    16 Control       F205--309 1. 1.

Iterating ...

  Iteration   1 LLik=    -33.419733
  Iteration   2 LLik=    -27.798546
  Iteration   3 LLik=    -27.681647
  Iteration   4 LLik=    -27.680482
  Iteration   5 LLik=    -27.680482

    Variable         Beta    Stand Error        t-Value
  -----------------------------------------------------
  apoe*3           1.8991         1.4611         1.2998 +
  apoe*4           3.2316         1.5727         2.0548 +

No. usable observations =     75 ( 31.0%)
    Number of affecteds =     40
  Number of unaffecteds =     35 (1 : 0.9)
       Number of strata =     16
       Conditional LRTS =     11.48
     Degrees of freedom =      2
     Asymptotic P-value =    0.3217E-02
             Score test =     10.83     (P=0.0044)

See also:

clreg

Conditional logistic regression