Reads molecular marker data and calculates IBD probabilities (M.P. Boer & J.T.N.M. Thissen).
Options
PRINT = string tokens |
What to print (summary, loci); default summ |
|---|---|
STEPSIZE = scalar |
Maximum stepsize along the genome; default 106, i.e. the IBD probabilities are calculated only at the marker positions |
METHOD = string token |
Method of calculation for IBD probabilities of RIL populations (approximate, exact); default appr |
POPULATIONTYPE = string token |
Type of population (BC1, DH1, F2, RIL, BCxSy, CP); must be set |
NGENERATIONS = scalar |
Number of generations of selfing for a RIL population |
NBACKCROSSES = scalar |
Number of backcrosses for a BCxSy population |
NSELFINGS = scalar |
Number of selfings for a BCxSy population |
MAPPINGFUNCTION = string token |
Mapping function (haldane, kosambi); default hald |
Parameters
MKSCORES = pointers |
Genotype codes for each marker; must be set |
|---|---|
CHROMOSOMES = factors |
The chromosome where each marker is located; must be set |
POSITIONS = variates |
The position on the chromosome of each marker; must be set |
MKNAMES = texts |
Marker names; must be set |
IDMGENOTYPES = texts |
Labels for the genotypes |
PARENTS = pointers |
Parent information; must be set |
IDPARENTS = texts |
Labels used to identify the parents; must be set |
PEDIGREE = pointers |
Defines the parents of the offspring |
ADDITIVEPREDICTORS = pointers |
Saves the additive genetic predictors |
ADD2PREDICTORS = pointers |
Saves the second (paternal) additive genetic predictors if POPULATIONTYPE is CP |
DOMINANCEPREDICTORS = pointers |
Saves the dominance genetic predictors if POPULATIONTYPE is F2, RIL, BCxSy or CP |
SCHROMOSOMES = factors |
Saves the chromosome where each locus is located |
SPOSITIONS = variates |
Saves the position on the chromosome of each locus |
LOCI = variates |
Saves the index number of each locus |
IDLOCI = texts |
Saves the locus labels |
MKLOCI = variates |
Saves a logical variate indicating whether each locus is a marker |
NLOCI = scalars |
Saves the number of loci |
NGENOTYPES = scalars |
Saves the number of genotypes |
APROBABILITIES = pointers |
Saves probabilities of the genotypes being equal to parent A |
BPROBABILITIES = pointers |
Saves probabilities of the genotypes being equal to parent B |
HPROBABILITIES = pointers |
Saves the probabilities of the genotypes being heterozygous |
ACPROBABILITIES = pointers |
Saves the probabilities of the genotypes being AC when POPULATIONTYPE is CP |
ADPROBABILITIES = pointers |
Saves the probabilities of the genotypes being AD when POPULATIONTYPE is CP |
BCPROBABILITIES = pointers |
Saves the probabilities of the genotypes being BC when POPULATIONTYPE is CP |
BDPROBABILITIES = pointers |
Saves the probabilities of the genotypes being BD when POPULATIONTYPE is CP |
OUTFILENAME = texts |
Name of the Genstat workbook file (*.gwb) to be created |
Description
QIBDPROBABILITIES calculates conditional genotypic probabilities at specific chromosome positions. The marker scores must be set by the MKSCORES parameter and the map data by the CHROMOSOMES, POSITIONS and MKNAMES parameters. The IDMGENOTYPES parameter can be set to label the genotypes. The marker scores of the parents must be set by the PARENTS parameter, and the corresponding labels of the parents must be set by the IDPARENTS parameter. The PEDIGREE parameter can provide a pointer containing factors to identify the parents of the offspring. This parameter must be set for multiple populations.
The POPULATIONTYPE option must specify the population type. For recombinant inbred lines (POPULATIONTYPE = RIL), the NGENERATIONS option specifies the number of generations; default 3. By default, with RIL populations, the conditional genotypic probabilities are calculated by an approximate method, but you can set option METHOD=exact to use an exact method instead. For backcross inbred lines (POPULATIONTYPE = BCxSy), the NBACKCROSSES and NSELFINGS options must be set to define the number of backcrosses to the first parent and the number of selfings, respectively.
The STEPSIZE option determines the maximum step size for the calculation of the conditional probabilities. A large value (like the default value 106) causes conditional probabilities to be calculated only at the marker positions.
The MAPPINGFUNCTION option defines the mapping function, which can be the Haldane or the Kosambi mapping function; default haldane.
For population types BC1, DH1, F2, RIL and BCxSy the calculated probabilities can be saved by the APROBABILITIES, BPROBABILITIES and HPROBABILITIES parameters: APROBABILITIES saves the probabilities that the genotypes are homozygous for the parent A allele, BPROBABILITIES saves the probabilities that the genotypes are homozygous for the parent B allele, and HPROBABILITIES saves the probabilities that the genotypes are heterozygous. From these probabilities the ADDITIVEPREDICTORS and the DOMINANCEPREDICTORS are calculated. For all population types, except backcross populations (BC1), the genetic predictors for the additive effects are given by
ADDITIVEPREDICTORS = APROBABILITIES - BPROBABILITIES
and
DOMINANCEPREDICTORS = HPROBABILITIES
For a backcross population (BC1), they are given by
ADDITIVEPREDICTORS = 0.5*APROBABILITIES - 0.5*BPROBABILITIES
For a cross pollinated population (CP), the parents are heterozygote. For a particular locus, let AB be the genotype of the first parent, and CD the genotype of the second parent, where allele A (C) is inherited from the mother of the first (second) parent, and allele B (D) is inherited from the father of the first (second) parent. The progeny can have 4 different genotypes, namely AC, AD, BC, and BD. The calculated probabilities corresponding to the four possible genotypes can be saved by the ACPROBABILITIES, ADPROBABILITIES, BCPROBABILITIES and BDPROBABILITIES parameters. The ADDITIVEPREDICTORS, ADD2PREDICTORS and the DOMINANCEPREDICTORS can be calculated from these probabilities, as follows. The genetic predictors for the maternal additive effects are given by
ADDITIVEPREDICTORS = BDPROBABILITIES + BCPROBABILITIES\
- ADPROBABILITIES - ACPROBABILITIESthe genetic predictors for the paternal additive effects by
ADD2PREDICTORS = BDPROBABILITIES - BCPROBABILITIES\
+ ADPROBABILITIES - ACPROBABILITIESand genetic predictors for the dominance effects by
DOMINANCEPREDICTORS = BDPROBABILITIES - BCPROBABILITIES\
- ADPROBABILITIES + ACPROBABILITIES
The number of chromosome positions (loci) where conditional probabilities have been estimated can be saved by the NLOCI parameter, and the number of genotypes can be saved by the NGENOTYPES parameter. The labels of the loci can be saved by the IDLOCI parameter. The CHROMOSOMES and POSITIONS parameters can save the map information of the loci: CHROMOSOMES saves the chromosome numbers, and POSITIONS saves the positions on the chromosome where conditional probabilities were calculated. A unique index number for each locus can be saved by the LOCI parameter. The MKLOCI parameter saves a logical variate storing one if the locus is a marker, otherwise zero.
The PRINT option controls the printed output. The summary setting prints the number of loci and the number of genotypes, and the loci setting prints all the loci index numbers together with the IDLOCI, CHROMOSOMES and POSITIONS values.
The OUTFILENAME parameter can be used to save the information in a Genstat workbook file. This parameter should not contain an extension as the extension is automatically set as .gwb. The LOCI, IDLOCI, CHROMOSOMES and POSITIONS structures are written to a sheet named LOCI, and the ADDITIVEPREDICTORS variates are written to a sheet named ADDPREDICTORS. The ADD2PREDICTORS and/or DOMINANCEPREDICTORS variates, when relevant, are written to sheets named ADD2PREDICTORS and DOMPREDICTORS respectively.
Options: PRINT, STEPSIZE, METHOD, POPULATIONTYPE, NGENERATIONS, NBACKCROSSES, NSELFINGS, MAPPINGFUNCTION.
Parameters: MKSCORES, CHROMOSOMES, POSITIONS, MKNAMES, IDMGENOTYPES, PARENTS, IDPARENTS, PEDIGREE, ADDITIVEPREDICTORS, ADD2PREDICTORS, DOMINANCEPREDICTORS, SCHROMOSOMES, SPOSITIONS, LOCI, IDLOCI, MKLOCI, NLOCI, NGENOTYPES, APROBABILITIES, BPROBABILITIES, HPROBABILITIES, ACPROBABILITIES, ADPROBABILITIES, BCPROBABILITIES, BDPROBABILITIES, OUTFILENAME.
Method
QIBDPROBABILITIES calls an external algorithm in the dynamic link library genetics.dll.
See also
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QIBDPROBABILITIES example'; STYLE=meta
" Steptoe x Morex (SxM)xM DH1 population "
QIMPORT [PRINT=*; POPULATIONTYPE=DH1]\
FILE='%GENDIR%/Examples/SxM_geno.txt';\
MAPFILE='%GENDIR%/Examples/SxM_map.txt';\
MKSCORES=mkscores; MKNAMES=mknames;\
PARENTS=parents; IDPARENT=idparent;\
CHROMOSOME=chromosomes; POSITIONS=positions
QIBDPROBABILITIES [PRINT=summary; STEPSIZE=10; POPULATIONTYPE=DH1]\
MKSCORES=mkscores; MKNAMES=mknames;\
CHROMOSOMES=chromosomes; POSITIONS=positions;\
PARENTS=parents; IDPARENT=idparent;\
SCHROMOSOME=mkchr; SPOSITIONS=mkpos;\
ADDITIVEPREDICTORS=addpred;\
OUTFILE='DH1_SxMmarkers'
" F2 population "
QIMPORT [PRINT=*; POPULATIONTYPE=F2]\
FILE='%GENDIR%/Examples/F2maize_geno.txt';\
MAPFILE='%GENDIR%/Examples/F2maize_map.txt';\
MKSCORES=mkscores; MKNAMES=mknames;\
PARENTS=parents; IDPARENT=idparent;\
CHROMOSOME=chromosomes; POSITIONS=positions
QIBDPROBABILITIES [PRINT=summary; STEPSIZE=10; POPULATIONTYPE=F2]\
MKSCORES=mkscores; MKNAMES=mknames;\
CHROMOSOMES=chromosomes; POSITIONS=positions;\
PARENTS=parents; IDPARENT=idparent;\
SCHROMOSOME=mkchr; SPOSITIONS=mkpos;\
IDLOCI=idlocus; ADDITIVEPREDICTORS=addpred;\
DOMINANCEPREDICTORS=dompred; OUTFILE='F2maizemarkers'
" cross pollinator "
QIMPORT [PRINT=*; POPULATIONTYPE=CP]\
FILE='%GENDIR%/Examples/CPapple_geno.txt';\
MAPFILE='%GENDIR%/Examples/CPapple_map.txt';\
MKSCORES=mkscores; MKNAMES=mknames;\
PARENTS=parents; IDPARENT=idparent;\
CHROMOSOME=chromosomes; POSITIONS=positions
QIBDPROBABILITIES [PRINT=summary; STEPSIZE=10; POPULATIONTYPE=CP]\
MKSCORES=mkscores; MKNAMES=mknames;\
CHROMOSOMES=chromosomes; POSITIONS=positions;\
PARENTS=parents; IDPARENT=idparent;\
SCHROMOSOME=mkchr; SPOSITIONS=mkpos;\
IDLOCI=idlocus; ADDITIVEPREDICTORS=addpred;\
ADD2PREDICTORS=add2pred; DOMINANCEPREDICTORS=dompred;\
OUTFILE='CPapplemarkers'