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)