[ < ] [ > ]   [ << ] [ Up ] [ >> ]         [Top] [Contents] [Index] [ ? ]

Statement Index

Jump to:   A   C   F   I   L   M   O   S   U  
Index Entry Section
A
allow component size2.4 Limit overriding
allow observed individuals2.4 Limit overriding
allow pedigree size2.4 Limit overriding
allow pedigree size2.9 Pedigree file description statements
assign gender3.5 pedcheck statements
assume all observed5.4.5 genedrop output pedigree options
C
check eigenvalue computation13.4.5 multivar output options
check eigenvalues13.4.5 multivar output options
check ginverse13.4.5 multivar output options
check gmatrix13.4.5 multivar output options
check marker consistency [only]9.8.1 Autozyg computing requests
check progress MC iterations8.6 MCMC parameter statements
check trace13.4.5 multivar output options
compute eigenvalues13.4.4 multivar computational options
compute estimates I times14.5 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
compute [component] inbreeding coefficient4.4 kin statements
compute [component] kinship coefficient4.4 kin statements
compute [component] two-locus inbreeding coefficient4.4 kin statements
F
fit additive correlations13.4.3 multivar computational parameters
fit additive covariances13.4.3 multivar computational parameters
fit environmental model13.4.4 multivar computational options
fit residual correlations13.4.3 multivar computational parameters
fit residual covariances13.4.3 multivar computational parameters
I
ignore gender3.5 pedcheck statements
input eigenvalue file13.4.3 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 gamete data file12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
input genotypes as rows12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
input haplotypes as columns of SNPs12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
input haplotypes as rows of SNPs12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
input individuals file2.3 File identification statements
input individuals record names traits reals11.9.3 Location lod scores pedigree file description
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)2.9 Pedigree file description statements
input pedigree record gender (present | absent)2.9 Pedigree file description statements
input pedigree record inheritance integer pairs6.5.5 markerdrop input file options
input pedigree record names 3 [integers] [reals]2.9 Pedigree file description statements
input pedigree record observed (absent | present)2.9 Pedigree file description statements
input pedigree record observed (absent | present)5.4.5 genedrop output pedigree options
input pedigree record trait integer pairs9.8.7 Autozyg computational parameters
input pedigree record traits integers2.9 Pedigree file description statements
input pedigree record traits integers6.5.5 markerdrop input file options
input pedigree record traits reals2.9 Pedigree file description statements
input pedigree record traits reals11.9.3 Location lod scores pedigree file description
input pedigree size2.9 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 iterations13.4.3 multivar computational parameters
limit EM iterations13.4.3 multivar computational parameters
limit recombination fractions L14.5 lm_map statements
M
map test tlocs no default external positions11.9.5 Location lod scores mapping model parameters
map test tlocs no default interval proportions11.9.5 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
map [chromosome] test tlocs jointly at markers11.9.5 Location lod scores mapping model parameters
map [chromosome] marker positions base pairs12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
map [chromosome] test tloc at markers11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] marker recombination fractions5.4.2 genedrop 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] test tloc all interval proportions11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc beginning recombination fractions11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc beginning [Kosambi] distance11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc ending recombination fractions11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc ending [Kosambi] distance11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc external distance11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc external Kosambi distance11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc external recombination fractions11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] test tloc intervals proportions11.9.5 Location lod scores mapping model parameters
map [chromosome][gender] tlocs marker recombination fractions5.4.2 genedrop 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 [gender] marker recombination fraction6.5.2 markerdrop 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] tlocs marker recombination fraction6.5.2 markerdrop mapping model parameters
map [gender] tlocs marker [Kosambi] distance6.5.2 markerdrop mapping model parameters
O
output all genotypes12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
output final adjusted phenotypes13.4.5 multivar output options
output final generation12.10.2 simpop_fgl parameter statements
output founder genome labels9.8.4 Autozyg output file description
output four-gamete state order jacquard12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
output four-gamete state order jacquard12.10.4 ibd_haplo parameter statements
output genotypes12.10.1 beaglesim and beagledag parameter statements
output haplotype labels12.10.1 beaglesim and beagledag parameter statements
output haplotype labels12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
output haplotypes as columns12.10.1 beaglesim and beagledag parameter statements
output haplotypes as rows12.10.1 beaglesim and beagledag parameter statements
output maps gender [averaged] [specific]14.5 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 chronological3.5 pedcheck statements
output pedigree file2.1 Command syntax
output pedigree record father mother3.5 pedcheck statements
output pedigree record founder gene labels5.4.5 genedrop output pedigree options
output pedigree record mother father3.5 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 file11.9.2 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 at markers12.10.4 ibd_haplo parameter statements
output scores every scored MC iterations9.8.4 Autozyg output file description
output seed file2.1 Command syntax
output spacing EM iterations13.4.5 multivar output options
output statistics correlations13.4.5 multivar output options
output statistics covariances13.4.5 multivar output options
output trait seeds only5.4.6 genedrop output seed file options
output with spaces12.10.1 beaglesim and beagledag parameter statements
output with spaces12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
output [overwrite] extra file2.3 File identification statements
output [overwrite] individuals file2.3 File identification statements
output [overwrite] individuals file3.5 pedcheck 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
Jump to:   A   C   F   I   L   M   O   S   U  
[ << ] [ >> ]           [Top] [Contents] [Index] [ ? ]

This document was generated by Elizabeth Thompson on September 6, 2019 using texi2html 1.82.