|
Column |
Description |
|
-d datafile |
Data File Name. Specifies that datafile
should be used as input data file. |
|
-p pedfile |
Pedigree File Name. Specifies that pedfile
should be used as the input pedigree file. |
|
-i ibdfile |
IBD File Name. Specifies that IBD information is stored
in ibdfile. |
|
-x miss |
Missing Value. Specifies that numeric values matching
miss should not be included in the analyses. |
|
-a[model] |
Association model. Common options include -a- (do
not model association), -aa (Allison's TDTQ5), -am
(Monks et al refinement of the Rabinowitz model) and -ao
(the orthogonal model of Abecasis et al, which we recommend!),
and -ad for a test using only affected individuals. |
|
-c[covariates] |
Covariates. Options include u (user-defined covariates
from the pedigree file), s (sex) and p (parental
phenotypes) and may be combined. |
|
-w[components] |
Variances model. Specify a model for the variances. Commonly
used variance components include the environmental variance (e),
polygenic variance (g) and additive major locus (a).
To select all three use -wega. |
|
-v[components] |
Another variances model. To compare two models for the
variances use this option as well as -w. For example,
to evaluate the significance of polygenic effects use specify
-we -veg. |
|
-n |
Numeric Minimizer. Select a numeric minimization strategy
for solving variance components problems. Available options are
-nf to use the Fletcher-Reeves refinement of the Polak-Ribiere
algorithm, -np to use Powell's conjugate directions method or
-nn to use the Nelder-Meed downhill simplex method. |
|
-t |
Transmission Scoring. Decide whether to score allelic
transmission using the complete pedigree (-tp) or within
nuclear families (-tn) |
|
-m9999 |
Permutations. Specify how many permutations should be
run to compute an empirical p-value. |
|
--dominance, -g |
Include a dominance parameter when modelling association. |
|
--snp, -1 |
Analysis of SNP data. Test only the first allele at each
marker. |
|
--multi-allelic, -9 |
Global test of association. Test for association considering
all alleles at a particular marker simultaneously, thereby reducing
multiple testing. |
|
--exclude-founder-phenotypes |
Excludes founder phenotypes when building regression or
variance components models. |
|
--p-values |
Display all p-values. By default, only p-values
of 0.10 or less are displayed. |
|
--deviates |
Phenotypes are deviates from population mean. Assume that the population
mean has been subtracted from each phenotype in the pedigree file. This option
is only suitable for the Monks and Rabinowitz tests and is useful in the analysis
of selected samples. |
|
-o[option] |
Parent of Origin Effects. |
