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Statement Index

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Index Entry Section

A
allow component size2.4 Limit overriding
allow observed individuals2.4 Limit overriding
allow pedigree size2.4 Limit overriding
allow pedigree size2.7 Pedigree file description statements
assign gender3.4 pedcheck statements
assume all observed5.4.5 genedrop output pedigree options

C
check eigenvalue computation12.4.5 multivar output options
check eigenvalues12.4.5 multivar output options
check ginverse12.4.5 multivar output options
check gmatrix12.4.5 multivar output options
check marker consistency [only]9.8.1 Autozyg computing requests
check progress MC iterations8.6 MCMC parameter statements
check trace12.4.5 multivar output options
compute [component] inbreeding coefficient4.4 kin statements
compute [component] kinship coefficient4.4 kin statements
compute [component] two-locus inbreeding coefficient4.4 kin statements
compute eigenvalues12.4.4 multivar computational options
compute estimates I times13.5 lm_map statements
compute ibd statistics10.6 lm_ibdtests and civil statements
compute likelihood-ratio statistics10.6 lm_ibdtests and civil statements
compute scores every iterations8.6 MCMC parameter statements

F
fit additive correlations12.4.3 multivar computational parameters
fit additive covariances12.4.3 multivar computational parameters
fit environmental model12.4.4 multivar computational options
fit residual correlations12.4.3 multivar computational parameters
fit residual covariances12.4.3 multivar computational parameters

I
ignore gender3.4 pedcheck statements
input eigenvalue file12.4.3 multivar computational parameters
input extra file2.1 Command syntax
input extra file2.3 File identification statements
input extra file10.6 lm_ibdtests and civil statements
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 mother | father mother)2.7 Pedigree file description statements
input pedigree record gender (present | absent)2.7 Pedigree file description statements
input pedigree record inheritance integer pairs6.5.5 markerdrop input file options
input pedigree record names 3 [integers] [reals]2.7 Pedigree file description statements
input pedigree record observed (absent | present)2.7 Pedigree file description statements
input pedigree record observed (absent | present)5.4.5 genedrop output pedigree options
input pedigree record traits integers2.7 Pedigree file description statements
input pedigree record traits integers6.5.5 markerdrop input file options
input pedigree record traits reals2.7 Pedigree file description statements
input pedigree record traits reals11.8.3 Location lod scores pedigree file description
input pedigree size2.7 Pedigree file description statements
input rescue file9.8.2 Autozyg file identification statements
input seed file2.1 Command syntax
input seed file2.3 File identification statements

L
limit breeding iterations12.4.3 multivar computational parameters
limit EM iterations12.4.3 multivar computational parameters
limit recombination fractions L13.5 lm_map statements

M
map [chromosome] test tlocs jointly at markers11.8.5 Location lod scores mapping model parameters
map [chromosome] test tloc at markers11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] marker [Kosambi] distances5.4.2 genedrop mapping model parameters
map [chromosome][gender] marker [Kosambi] positions5.4.2 genedrop mapping model parameters
map [chromosome][gender] marker recombination fractions5.4.2 genedrop mapping model parameters
map [chromosome][gender] test tloc all interval proportions11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc beginning [Kosambi] distance11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc beginning recombination fractions11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc ending [Kosambi] distance11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc ending recombination fractions11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc external distance11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc external Kosambi distance11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc external recombination fractions11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc intervals proportions11.8.5 Location lod scores mapping model parameters
map [chromosome][gender] tlocs marker [Kosambi] distances5.4.2 genedrop mapping model parameters
map [chromosome][gender] tlocs marker [Kosambi] positions5.4.2 genedrop mapping model parameters
map [chromosome][gender] tlocs marker recombination fractions5.4.2 genedrop mapping model parameters
map [gender] marker [Kosambi] distance6.5.2 markerdrop mapping model parameters
map [gender] marker [Kosambi] position6.5.2 markerdrop mapping model parameters
map [gender] marker recombination fraction6.5.2 markerdrop mapping model parameters
map [gender] tlocs marker [Kosambi] distance6.5.2 markerdrop mapping model parameters
map [gender] tlocs marker recombination fraction6.5.2 markerdrop mapping model parameters
map test tlocs no default external positions11.8.5 Location lod scores mapping model parameters
map test tlocs no default interval proportions11.8.5 Location lod scores mapping model parameters
map tlocs unlinked5.4.1 genedrop computing requests
map tlocs unlinked7.4 ibddrop statements
map tlocs unlinked9.8.1 Autozyg computing requests

O
output [overwrite] extra file2.3 File identification statements
output [overwrite] pedigree file2.3 File identification statements
output [overwrite] score file2.3 File identification statements
output [overwrite] score file9.8.2 Autozyg file identification statements
output [overwrite] seed file2.3 File identification statements
output final adjusted phenotypes12.4.5 multivar output options
output founder genome labels9.8.4 Autozyg output file description
output maps gender [averaged] [specific]13.5 lm_map statements
output marker seeds only5.4.6 genedrop output seed file options
output meiosis indicators9.8.4 Autozyg output file description
output pedigree chronological3.4 pedcheck statements
output pedigree file2.1 Command syntax
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 permutation seeds only10.6 lm_ibdtests and civil statements
output Rao-Blackwellized estimates file11.8.2 Location lod scores file identification statements
output rescue data iterations9.8.4 Autozyg output file description
output rescue file9.8.2 Autozyg file identification statements
output sampler seeds only10.6 lm_ibdtests and civil statements
output scores every scored MC iterations9.8.4 Autozyg output file description
output seed file2.1 Command syntax
output spacing EM iterations12.4.5 multivar output options
output statistics correlations12.4.5 multivar output options
output statistics covariances12.4.5 multivar output options
output trait seeds only5.4.6 genedrop output seed file options

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