Replaces missing molecular marker scores using conditional genotypic probabilities (D.A. Murray, M. Malosetti & M.P. Boer).
Options
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 |
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 |
NEWMKSCORES = pointers |
Saves the imputed genotype codes for each marker; if this is not set, the imputed values overwrite those in MKSCORES |
Description
QMVESTIMATE replaces missing marker scores using the conditional genotypic probabilities evaluated at specific chromosome positions. The marker scores containing the missing observations must be supplied in a pointer to a set of factors using the MKSCORES parameter. The linkage groups for each marker are supplied in a factor by the CHROMOSOMES parameter. The names of the markers are supplied in a text using the MKNAMES parameter, and the marker positions are supplied in a variate using the POSITIONS parameter. The IDMGENOTYPES parameter to label the genotypes should be supplied within a text. The parent information should be supplied in a pointer to a set of texts using the PARENTS parameter, and the labels for the parents should be supplied in a text using the IDPARENTS parameter. The marker scores containing the replaced missing observations can be saved within a pointer to a set of factors using the NEWMKSCORES parameter. If the NEWMKSCORES parameter is not set, then the missing marker scores are replaced in the MKSCORES.
The POPULATIONTYPE option must 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 and NSELFINGS options must be set to define the number of backcrosses to the first parent and the number of selfings, respectively.
Options: POPULATIONTYPE, NGENERATIONS, NBACKCROSSES, NSELFINGS.
Parameters: MKSCORES, CHROMOSOMES, POSITIONS, MKNAMES, IDMGENOTYPES, PARENTS, IDPARENTS, NEWMKSCORES.
Method
QMVESTIMATE calls QIBDPROBABILITIES to calculate the conditional probabilities.
See also
Procedures: QIBDPROBABILITIES, QMVREPLACE.
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QMVESTIMATE example'; STYLE=meta
" 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; IDMGENOTYPES=idgeno;\
CHROMOSOME=chromosomes; POSITIONS=positions
QMVESTIMATE [POPULATIONTYPE=F2]\
MKSCORES=mkscores; MKNAMES=mknames;\
CHROMOSOMES=chromosomes; POSITIONS=positions;\
PARENTS=parents; IDPARENT=idparent; IDMGENOTYPES=idgeno;\
NEWMKSCORES=newscores
RESTRICT mkscores[1,3,4],newscores[1,3,4];\
(mkscores[1].IN.'-/-').OR.(mkscores[3].IN.'-/-').OR.\
(mkscores[4].IN.'-/-')
PRINT mkscores[1],newscores[1],mkscores[3],newscores[3],\
mkscores[4],newscores[4]; FIELD=13
RESTRICT mkscores[1,3,4],newscores[1,3,4]