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 10^{6}, 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 10^{6}) 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 - ACPROBABILITIES`

the genetic predictors for the paternal additive effects by

`ADD2PREDICTORS = BDPROBABILITIES - BCPROBABILITIES\`

` + ADPROBABILITIES - ACPROBABILITIES`

and 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'