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Statement Index

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Index Entry Section

A
allow pedigree size2.5 Pedigree file description statements
assign gender3.4 pedcheck statements
assume all observed5.4.5 genedrop output pedigree options

C
check eigenvalue computation9.4.5 multivar output options
check eigenvalues9.4.5 multivar output options
check ginverse9.4.5 multivar output options
check gmatrix9.4.5 multivar output options
check progress MC iterations7.6.5 Autozyg MCMC parameters and options
check trace9.4.5 multivar output options
component compute two-locus inbreeding coefficient4.4 kin statements
compute component inbreeding coefficient4.4 kin statements
compute component kinship coefficient4.4 kin statements
compute eigenvalues9.4.4 multivar computational options
compute inbreeding coefficient4.4 kin statements
compute kinship coefficient4.4 kin statements
compute scores every iterations7.6.5 Autozyg MCMC parameters and options
compute two-locus inbreeding coefficient4.4 kin statements

F
fit additive correlations9.4.3 multivar computational parameters
fit additive covariances9.4.3 multivar computational parameters
fit environmental model9.4.4 multivar computational options
fit residual correlations9.4.3 multivar computational parameters
fit residual covariances9.4.3 multivar computational parameters

I
ignore gender3.4 pedcheck statements
input eigenvalue file9.4.3 multivar computational parameters
input marker data file2.1 Command syntax
input marker data file2.3 File identification statements
input pedigree file2.1 Command syntax
input pedigree file2.3 File identification statements
input pedigree record father mother2.5 Pedigree file description statements
input pedigree record gender absent2.5 Pedigree file description statements
input pedigree record gender present2.5 Pedigree file description statements
input pedigree record mother father2.5 Pedigree file description statements
input pedigree record names 32.5 Pedigree file description statements
input pedigree record names 3 integers2.5 Pedigree file description statements
input pedigree record names 3 integers reals2.5 Pedigree file description statements
input pedigree record observed absent5.4.5 genedrop output pedigree options
input pedigree record observed present5.4.5 genedrop output pedigree options
input pedigree record traits integers2.5 Pedigree file description statements
input pedigree size2.5 Pedigree file description statements
input seed file2.1 Command syntax
input seed file2.3 File identification statements

L
limit breeding iterations9.4.3 multivar computational parameters
limit EM iterations9.4.3 multivar computational parameters

M
map chromosome gender marker distance5.4.2 genedrop mapping model parameters
map chromosome gender marker positions5.4.2 genedrop mapping model parameters
map chromosome gender marker recombination fractions5.4.2 genedrop mapping model parameters
map chromosome gender trait all interval proportions8.8.2 Location LOD scores mapping model parameters
map chromosome gender trait beginning distance8.8.2 Location LOD scores mapping model parameters
map chromosome gender trait beginning recombination fractions8.8.2 Location LOD scores mapping model parameters
map chromosome gender trait ending distance8.8.2 Location LOD scores mapping model parameters
map chromosome gender trait ending recombination fractions8.8.2 Location LOD scores mapping model parameters
map chromosome gender trait external distance8.8.2 Location LOD scores mapping model parameters
map chromosome gender trait external recombination fractions8.8.2 Location LOD scores mapping model parameters
map chromosome gender trait intervals proportions8.8.2 Location LOD scores mapping model parameters
map chromosome gender traits marker distances5.4.2 genedrop mapping model parameters
map chromosome gender traits marker recombination fractions5.4.2 genedrop mapping model parameters
map chromosome marker distances5.4.2 genedrop mapping model parameters
map chromosome marker positions5.4.2 genedrop mapping model parameters
map chromosome marker recombination fractions5.4.2 genedrop mapping model parameters
map chromosome trait all interval proportions8.8.2 Location LOD scores mapping model parameters
map chromosome trait beginning distance8.8.2 Location LOD scores mapping model parameters
map chromosome trait beginning recombination fractions8.8.2 Location LOD scores mapping model parameters
map chromosome trait ending distance8.8.2 Location LOD scores mapping model parameters
map chromosome trait ending recombination fractions8.8.2 Location LOD scores mapping model parameters
map chromosome trait external distance8.8.2 Location LOD scores mapping model parameters
map chromosome trait external recombination fractions8.8.2 Location LOD scores mapping model parameters
map chromosome trait intervals proportions8.8.2 Location LOD scores mapping model parameters
map chromosome traits marker distances5.4.2 genedrop mapping model parameters
map chromosome traits marker recombination fractions5.4.2 genedrop mapping model parameters
map gender marker distances5.4.2 genedrop mapping model parameters
map gender marker positions5.4.2 genedrop mapping model parameters
map gender marker recombination fractions5.4.2 genedrop mapping model parameters
map gender trait all interval proportions8.8.2 Location LOD scores mapping model parameters
map gender trait beginning distance8.8.2 Location LOD scores mapping model parameters
map gender trait beginning recombination fractions8.8.2 Location LOD scores mapping model parameters
map gender trait ending distance8.8.2 Location LOD scores mapping model parameters
map gender trait ending recombination fractions8.8.2 Location LOD scores mapping model parameters
map gender trait external distance8.8.2 Location LOD scores mapping model parameters
map gender trait external recombination fractions8.8.2 Location LOD scores mapping model parameters
map gender trait intervals proportions8.8.2 Location LOD scores mapping model parameters
map gender traits marker distances5.4.2 genedrop mapping model parameters
map gender traits marker recombination fractions5.4.2 genedrop mapping model parameters
map marker distances5.4.2 genedrop mapping model parameters
map marker positions5.4.2 genedrop mapping model parameters
map marker recombination fractions5.4.2 genedrop mapping model parameters
map trait all interval proportions8.8.2 Location LOD scores mapping model parameters
map trait beginning distance8.8.2 Location LOD scores mapping model parameters
map trait beginning recombination fractions8.8.2 Location LOD scores mapping model parameters
map trait ending distance8.8.2 Location LOD scores mapping model parameters
map trait ending recombination fractions8.8.2 Location LOD scores mapping model parameters
map trait external distance8.8.2 Location LOD scores mapping model parameters
map trait external recombination fractions8.8.2 Location LOD scores mapping model parameters
map trait intervals proportions8.8.2 Location LOD scores mapping model parameters
map traits marker distances5.4.2 genedrop mapping model parameters
map traits marker recombination fractions5.4.2 genedrop mapping model parameters

O
output final adjusted phenotypes9.4.5 multivar output options
output marker seeds only5.4.6 genedrop output seed file options
output pedigree chronological3.4 pedcheck statements
output pedigree file2.1 Command syntax
output pedigree file2.3 File identification statements
output pedigree record father mother3.4 pedcheck statements
output pedigree record founder gene labels5.4.5 genedrop output pedigree options
output pedigree record mother father3.4 pedcheck statements
output pedigree record trait latent variables5.4.5 genedrop output pedigree options
output pedigree record unobserved variables5.4.5 genedrop output pedigree options
output score file2.1 Command syntax
output seed file2.1 Command syntax
output seed file2.3 File identification statements
output spacing EM iterations9.4.5 multivar output options
output statistics correlations9.4.5 multivar output options
output statistics covariances9.4.5 multivar output options
output trait seeds only5.4.6 genedrop output seed file options

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