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Statement Index: S

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Index Entry Section
S
sample by scan8.6 MCMC parameter statements
sample by step8.6 MCMC parameter statements
select inheritance6.5.1 markerdrop computing requests
select partially phased data12.10.4 ibd_haplo parameter statements
select phased data12.10.4 ibd_haplo parameter statements
select state transition matrix12.10.4 ibd_haplo parameter statements
select trait6.5.1 markerdrop computing requests
select trait9.8.1 Autozyg computing requests
select trait9.8.7 Autozyg computational parameters
select trait13.4.1 multivar computing requests
select unphased data12.10.4 ibd_haplo parameter statements
select [chromosome] all markers9.8.1 Autozyg computing requests
select [chromosome] all markers except9.8.1 Autozyg computing requests
select [chromosome] markers9.8.1 Autozyg computing requests
set batches MC variance estimation11.9.7 Location lod scores computational parameters
set base log likelihood11.9.7 Location lod scores computational parameters
set breeding convergence13.4.3 multivar computational parameters
set burn-in iterations8.6 MCMC parameter statements
set chromosome length centiMorgans12.10.2 simpop_fgl parameter statements
set debug level2.6 Output control
set debug libname2.6 Output control
set debug main2.6 Output control
set dummy integers2.5 Input extra variables
set dummy reals2.5 Input extra variables
set eigenvalues13.4.3 multivar computational parameters
set EM convergence14.5 lm_map statements
set females per generation12.10.2 simpop_fgl parameter statements
set genotyping error rate12.10.4 ibd_haplo parameter statements
set genotyping error rate14.5 lm_map statements
set global MCMC8.6 MCMC parameter statements
set ibd measures10.6 lm_ibdtests and civil statements
set ibd permutations10.6 lm_ibdtests and civil statements
set ibd tests10.6 lm_ibdtests and civil statements
set inheritance tlocs6.5.1 markerdrop computing requests
set kinship change rate12.10.4 ibd_haplo parameter statements
set L-sampler probability8.6 MCMC parameter statements
set LD relaxation probability12.10.1 beaglesim and beagledag parameter statements
set liability classes with penetrances9.8.7 Autozyg computational parameters
set likelihood-ratio lambda-p model gridpoints10.6 lm_ibdtests and civil statements
set likelihood-ratio measures10.6 lm_ibdtests and civil statements
set likelihood-ratio tests10.6 lm_ibdtests and civil statements
set limit for exact computation8.6 MCMC parameter statements
set LRT statistics iterations14.5 lm_map statements
set map estimation with [no] mistyping14.5 lm_map statements
set marker data9.8.7 Autozyg computational parameters
set marker seeds5.4.4 genedrop computational parameters
set maximum ibdgraphs per component11.9.7 Location lod scores computational parameters
set MC iterations8.6 MCMC parameter statements
set MC iterations11.9.8 Location lod scores MCMC parameters and options
set MCMC markers only9.8.8 Autozyg MCMC parameters and options
set million base pairs per centiMorgan12.10.3 fgl2ibd and fgl2haplo and fgl2dgl parameter statements
set normalized allele frequencies5.4.3 genedrop population model parameters
set number of permutations11.9.7 Location lod scores computational parameters
set offspring generations12.10.2 simpop_fgl parameter statements
set permutation seeds10.6 lm_ibdtests and civil statements
set population kinship12.10.4 ibd_haplo parameter statements
set printlevel2.6 Output control
set proband gametes all individual pairs12.10.4 ibd_haplo parameter statements
set pseudo-prior iterations11.9.8 Location lod scores MCMC parameters and options
set pseudo-priors11.9.7 Location lod scores computational parameters
set recombination frequencies4.4 kin statements
set remating probability weight12.10.2 simpop_fgl parameter statements
set SA ascent iterations14.5 lm_map statements
set SA convergence14.5 lm_map statements
set SA curvature iterations14.5 lm_map statements
set SA gradient iterations14.5 lm_map statements
set sampler seeds7.4 ibddrop statements
set sequential imputation proposals every iterations11.9.8 Location lod scores MCMC parameters and options
set standard deviations for genotypes9.8.7 Autozyg computational parameters
set test position window11.9.8 Location lod scores MCMC parameters and options
set tlocs allele frequencies5.4.3 genedrop population model parameters
set tlocs allele frequencies6.5.3 markerdrop population model parameters
set trait data9.8.7 Autozyg computational parameters
set trait data discrete6.5.4 markerdrop computational parameters
set trait data discrete with covariate9.8.7 Autozyg computational parameters
set trait data discrete with liability9.8.7 Autozyg computational parameters
set trait effects13.4.1 multivar computing requests
set trait for tlocs joint genotype means11.9.7 Location lod scores computational parameters
set trait seeds5.4.4 genedrop computational parameters
set traits additive variance5.4.3 genedrop population model parameters
set traits for tlocs genotype means5.4.3 genedrop population model parameters
set traits for tlocs incomplete penetrances6.5.4 markerdrop computational parameters
set traits for tlocs incomplete penetrances9.8.7 Autozyg computational parameters
set traits multiple tlocs11.9.7 Location lod scores computational parameters
set traits residual variance5.4.3 genedrop population model parameters
set traits tlocs5.4.1 genedrop computing requests
set traits tlocs6.5.1 markerdrop computing requests
set traits tlocs9.8.1 Autozyg computing requests
set transition matrix null fraction12.10.4 ibd_haplo parameter statements
set width of ages of onset window9.8.7 Autozyg computational parameters
set [chromosome] locus window7.4 ibddrop statements
set [chromosome] locus window9.8.7 Autozyg computational parameters
set [chromosome] marker allele frequencies5.4.3 genedrop population model parameters
set [chromosome] marker allele frequencies6.5.3 markerdrop population model parameters
set [chromosome] marker names6.5.3 markerdrop population model parameters
set [chromosome] marker names9.8.6 Autozyg population model parameters
set [component] proband gametes7.4 ibddrop statements
set [component] proband gametes9.8.7 Autozyg computational parameters
set [component] [scoreset] proband gametes9.8.7 Autozyg computational parameters
set [component] [scoreset] window patterns9.8.7 Autozyg computational parameters
set [scoreset] proband gametes12.10.4 ibd_haplo parameter statements
simulate ibd realizations7.4 ibddrop statements
simulate ibd realizations11.9.7 Location lod scores computational parameters
simulate IBD realizations for trait11.9.7 Location lod scores computational parameters
simulate tloc7.4 ibddrop statements
simulate traits5.4.1 genedrop computing requests
simulate [chromosome] markers5.4.1 genedrop computing requests
simulate [chromosome] [dense] markers6.5.1 markerdrop computing requests
simulate [chromosome] [dense] markers7.4 ibddrop statements
start additive correlations13.4.2 multivar segregation model parameters
start additive covariances13.4.2 multivar segregation model parameters
start additive variances13.4.2 multivar segregation model parameters
start residual correlations13.4.2 multivar segregation model parameters
start residual covariances13.4.2 multivar segregation model parameters
start residual variances13.4.2 multivar segregation model parameters
start trait effect13.4.2 multivar segregation model parameters
start trait mean13.4.2 multivar segregation model parameters
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