| bt {gap} | R Documentation |
This function calculates statistics under Bradley-Terry model.
bt(x)
x |
the data table |
The returned value is a list containing:
y |
A column of 1 |
count |
the frequency count/weight |
allele |
the design matrix |
bt.glm |
a glm.fit object |
etdt.dat |
a data table that can be used by ETDT |
Bradley RA, Terry ME (1952) Rank analysis of incomplete block designs I. the method of paired comparisons. Biometrika 39:324–345
Sham PC, Curtis D (1995) An extended transmission/disequilibrium test ({TDT}) for multi-allelic marker loci. Ann. Hum. Genet. 59:323-336
/*Adapted from the SAS macro below for data in the example section*/
%macro mtdt(data,n);
data _bt_;
set &data;
array x {&n} x1-x&n;
array allele {&n} y1-y&n;
do i=1 to &n; allele{i}=0; end;
y=1;
do i=1 to &n;
allele{_n_}=1;
allele{i}=-1;
count=x{i};
if _n_ ne i then output;
allele{i}=0;
end;
keep y count y1-y&n;
run;
/*Bradly-Terry model*/
proc logistic data=_bt_;
freq count;
model y=y1-y&n / noint;
output out=out p=p;
run;
/*Bowker's test of symmetry*/
data b;
array x x1-x&n;
do i=1 to &n;
set &data;
do j=1 to &n; w=x[j]; output; end;
end;
drop x1-x&n;
run;
proc freq;
weight w;
table i*j / agree noprint;
run;
%mend;
data a;
input x1-x12;
cards;
0 0 0 2 0 0 0 0 0 0 0 0
0 0 1 3 0 0 0 2 3 0 0 0
2 3 26 35 7 0 2 10 11 3 4 1
2 3 22 26 6 2 4 4 10 2 2 0
0 1 7 10 2 0 0 2 2 1 1 0
0 0 1 4 0 1 0 1 0 0 0 0
0 2 5 4 1 1 0 0 0 2 0 0
0 0 2 6 1 0 2 0 2 0 0 0
0 3 6 19 6 0 0 2 5 3 0 0
0 0 3 1 1 0 0 0 1 0 0 0
0 0 0 2 0 0 0 0 0 0 0 0
0 0 1 0 0 0 0 0 0 0 0 0
;
%mtdt(a,12);
Jing Hua Zhao
## Not run:
# Copeman JB, Cucca F, Hearne CM, Cornall RJ, Reed PW,
# Ronningen KS, Undlien DE, Nistico L, Buzzetti R, Tosi R, et al.
# (1995) Linkage disequilibrium mapping of a type 1
# diabetes susceptibility gene (IDDM7) to chromosome 2q31-q33.
# Nat Genet 9: 80-5
x <- matrix(c(0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
0,0, 1, 3, 0,0, 0, 2, 3, 0, 0, 0,
2,3,26,35, 7,0, 2,10,11, 3, 4, 1,
2,3,22,26, 6,2, 4, 4,10, 2, 2, 0,
0,1, 7,10, 2,0, 0, 2, 2, 1, 1, 0,
0,0, 1, 4, 0,1, 0, 1, 0, 0, 0, 0,
0,2, 5, 4, 1,1, 0, 0, 0, 2, 0, 0,
0,0, 2, 6, 1,0, 2, 0, 2, 0, 0, 0,
0,3, 6,19, 6,0, 0, 2, 5, 3, 0, 0,
0,0, 3, 1, 1,0, 0, 0, 1, 0, 0, 0,
0,0, 0, 2, 0,0, 0, 0, 0, 0, 0, 0,
0,0, 1, 0, 0,0, 0, 0, 0, 0, 0, 0),nrow=12)
# Bradley-Terry model, only deviance is available in glm
# (SAS gives score and Wald statistics as well)
bt.ex<-bt(x)
anova(bt.ex$bt.glm)
summary(bt.ex$bt.glm)
## End(Not run)