Simulates marker data and QTL effects for single and multiple environment trials (M.P. Boer & J.T.N.M. Thissen).
Options
PRINT = string token |
What to print (summary); default summ |
|---|---|
POPULATIONTYPE = string token |
Type of population (BC1, DH1, F2, RIL, BCxSy, CP); must be set |
NGENERATIONS = scalar |
Number of generations for a RIL population; default 3 |
NBACKCROSSES = scalar |
Number of backcrosses for a BCxSy population; default 2 |
NSELFINGS = scalar |
Number of selfings for a BCxSy population; default 3 |
GENOMELENGTH = variate |
Length in cM for each chromosome |
DISTANCE = scalar |
Distance between the markers in cM; default 1 cM |
COMPLETE = string token |
Complete marker information, i.e. all parents have a different allele (yes, no); default no |
FRACTIONMISSING = scalar |
Fraction of the markers with missing values; default 0 |
NGENOTYPES = scalar |
Number of genotypes; must be set |
NCHROMOSOMES = scalar |
Number of chromosomes |
NPOSITIONS = scalar |
Number of positions per chromosome |
IDPARENTS = texts |
Labels used to identify the parents |
MEAN = scalar or variate |
Mean of the trait for each environment; must be set if TRAIT is set |
VARIANCE = scalar or variate |
Variance of the trait for each environment; must be set if TRAIT is set |
ADDITIVEEFFECTS = variate or pointer |
Additive effects of each QTL for each environment; must be set if TRAIT is set |
ADD2PREDICTORS = pointers |
Second (paternal) set of additive genetic predictors of each QTL for each environment if POPULATIONTYPE is CP; must be set if TRAIT is set |
DOMINANCEPREDICTORS = pointers |
Dominance genetic predictors of each QTL for each environment if POPULATIONTYPE is F2 or CP; must be set if TRAIT is set |
QTLCHROMOSOMES = variate |
Chromosome number for each QTL; must be set if TRAIT is set |
QTLPOSITIONS = variate |
Position on the QTLCHROMOSOMES for each QTL; must be set if TRAIT is set |
Parameters
TRAIT = variates |
Saves the quantitative trait values |
|---|---|
GENOTYPES = factors |
Saves the genotype factor |
ENVIRONMENTS = factors |
Saves the environment factor |
MKSCORES = pointers |
Saves the marker scores for each marker |
CHROMOSOMES = factors |
Saves the linkage groups of the markers |
POSITIONS = variates |
Saves the position on the chromosome for each marker |
MKNAMES = texts |
Names of the markers |
IDMGENOTYPES = texts |
Labels of the genotypes |
PARENTS = pointers |
Saves the parent information |
SEED = scalars |
Specifies a seed to use for the random number generator; default 0 continues from the previous generation or (if none) initializes the seed automatically |
Description
QSIMULATE can be used to simulate marker data and/or QTL effects, for either single or multiple environment trials. The specification of the simulation is defined by the options, and the parameters save each set of simulated data.
The PRINT option controls printed output. There is a single setting, summary, which prints a summary of the simulations; this is the default.
The POPULATIONTYPE option must be set to specify the population type. For recombinant inbred lines (POPULATIONTYPE=RIL), the NGENERATIONS option specifies the number of generations; default 3. For backcross inbred lines (POPULATIONTYPE=BCxSy), the NBACKCROSSES option specifies the number of backcrosses, and the NSELFINGS option specifies the number of selfings.
The GENOMELENGTH option can be used to supply a variate specifying the length of the chromosomes, and DISTANCE option defines the distance between the markers in cM. Alternatively, instead supplying the GENOMELENGTH variate, you can define the genome using the NCHROMOSOMES and NPOSITIONS options. The NGENOTYPES option must be set to define the number of genotypes. If marker scores for the PARENTS are also to be simulated, the IDPARENTS option can be used to label the parents.
The MEAN option defines the overall mean of the trait, as scalar for a single environment or a variate for multi-environment trials. The VARIANCE option defines the error variance for the environments. The positions of the QTLs are defined by the QTLCHROMOSOMES and QTLPOSITIONS options. The ADDITIVEEFFECTS, ADD2EFFECTS and DOMINANCEEFFECTS options define the additive, second additive and dominance effects of the simulated QTLs.
Setting option COMPLETE=yes specifies that the parents all have a different allele for the markers. With the default setting, no the markers are assumed to be SNPs, and the marker score for a parent is either 1 or 2 with equal probabilities. For a bi-parental cross this means that around 50% of the markers will be polymorphic. The FRACTIONMISSING option can be used to define a fraction of missing marker scores. The default is that no scores are missing (FRACTIONMISSING=0).
The SEED parameter can be set to specify a seed for the random number generator for each set of simulated data. The MARKERSCORES parameter saves the simulated marker scores for all the markers and all the offspring. The MARKERNAMES parameter saves the names of the simulated markers. The IDMGENOTYPES parameter saves the labels of all the genotypes. The CHROMOSOMES and POSITIONS parameters save the chromosomes and positions of the simulated markers, and the PARENTS parameter saves the marker scores for the parents. The TRAIT parameter saves the simulated trait data, for all the genotypes and for all the environments. The ENVIRONMENTS and GENOTYPES factors save the corresponding environments and genotypes for the simulated TRAIT parameter.
Options: PRINT, POPULATIONTYPE, NGENERATIONS, NBACKCROSSES, NSELFINGS, GENOMELENGTH, DISTANCE, COMPLETE, FRACTIONMISSING, NGENOTYPES, NCHROMOSOMES, NPOSITIONS, IDPARENTS, MEAN, VARIANCE, ADDITIVEEFFECTS, ADD2EFFECTS, DOMINANCEEFFECTS, QTLCHROMOSOMES, QTLPOSITIONS.
Parameters: TRAIT, GENOTYPES, ENVIRONMENTS, MKSCORES, CHROMOSOMES, POSITIONS, MKNAMES, IDMGENOTYPES, PARENTS, SEED.
Method
QSIMULATE calls an external algorithm in the dynamic link library genetics.dll.
Action with RESTRICT
Restrictions are not allowed.
See also
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QSIMULATE example'; STYLE=meta
TEXT [NVALUES=2] idparents; VALUES=!t('Cvi','Ler')
VARIATE [NVALUES=5] genome; VALUES=!(150,100,120,90,130)
VARIATE [NVALUES=4] popmean; VALUES=!(10.0,11.0,12.0, 9.0)
VARIATE [NVALUES=4] errorvar; VALUES=!(25.0,20.0,30.0,15.0)
"QTL positions:"
VARIATE [NVALUES=3] QTLchr; VALUES=!(1,2,5)
VARIATE [NVALUES=3] QTLpos; VALUES=!(49.7,59.3,71.5)
"addditive effects QTLs for 4 environments:"
VARIATE [NVALUES=3] addeff[1]; VALUES=!(2.0,2.0,-1.5)
VARIATE [NVALUES=3] addeff[2]; VALUES=!(2.0,1.5,-0.5)
VARIATE [NVALUES=3] addeff[3]; VALUES=!(2.0,1.0, 0.5)
VARIATE [NVALUES=3] addeff[4]; VALUES=!(2.0,0.5, 1.5)
QSIMULATE [POPULATION=DH1; DISTANCE=2.5; GENOME=genome; NGENOTYPES=200;\
QTLCHROMOSOMES=QTLchr; QTLPOSITIONS=QTLpos;\
MEAN=popmean; VARIANCE=errorvar;\
ADDITIVEEFFECT=addeff; IDPARENTS=idparents]\
TRAIT=trait; GENOTYPES=geno; ENVIRONMENTS=env;\
MKSCORES=mk_scores; CHROMOSOMES=mk_chr; POSITIONS=mk_pos;\
MKNAMES =mk_names; IDMGENOTYPES=idm_geno;\
PARENTS=parents; SEED=4098
EXPORT [OUTFILE='simDH1_pheno.gsh'; METHOD=overwrite] env,geno,trait
QEXPORT [OUTFILENAME='simDH1_geno.txt'; MAPFILENAME='simDH1_map.txt';\
POPULATION=DH1] MKSCORES=mk_scores; CHROMOSOMES=mk_chr;\
POSITIONS=mk_pos; MKNAMES=mk_names;\
IDMGENOTYPES=idm_geno; IDPARENTS=idparents; PARENTS=parents
QIMPORT [PRINT=catalog; POPULATION=DH1] 'simDH1_geno.txt';\
MAPFILENAME='simDH1_map.txt'; MKSCORES=mkscores
IMPORT 'simDH1_pheno.gsh'