Obtains a representative selection of markers by means of genetic distance sampling or genetic distance optimization (J. Jansen & J.T.N.M. Thissen).
|What to print (
||The number of markers to be selected; must be set|
||Method to be used (
||Names of the markers; must be set|
||Input recombination frequencies matrix for each selection; must be set|
||Defines prior groupings of the markers|
||Logical variate indicating whether a marker is selected (1) as cluster centre or not (0)|
||Saves the nearest cluster centres of the markers|
||Saves the distances of the markers to the nearest cluster centre|
||Seed for randomization at the start; default 0|
QMKSELECT selects a representative subset of markers using a matrix of recombination frequencies, provided by the
METHOD option specifies whether to use genetic distance sampling or genetic distance optimization, by setting it to one of the following settings:
||genetic distance sampling using the method of Jansen & Van Hintum (2006), or|
||genetic distance optimization based on K-medoids cluster analysis (Kaufman & Rouseeuw 1990).|
The default is
The marker names must be supplied by the
MKNAMES parameter, and the number of markers to be selected must be specified by the
NCLUSTERS option. Prior information about the grouping of the markers can be supplied using the
SEED parameter specifies the seed to use to randomize the markers at the start. The default value of zero continues an existing sequence, or (if none) initializes the seed automatically.
The marker selection can be saved by the
SELECTED parameter, in a logical variate containing one for each marker selected as a cluster centre, and zero for the markers that are not selected. The
NEIGHBOURS parameter saves the nearest cluster centre for each marker, and the
DISTANCES parameter saves the distances of each marker to the nearest cluster centre.
||for a summary of the selection, and|
||for monitoring information.|
Restrictions are not allowed.
Jansen, J. & Th.J.L. van Hintum (2006). Genetic distance sampling: a novel sampling method for obtaining core collections using genetic distances with an application to cultivated lettuce. Theor. Appl. Genet., 114, 421-428.
Kaufman, P. & P.J. Rousseuw (1990). Finding Groups in Data: an Introduction to Cluster Analysis. Wiley, New York.
Commands for: Statistical genetics and QTL estimation.
CAPTION 'QMKSELECT example'; STYLE=meta QIMPORT [POPULATION=F2] '%GENDIR%/Examples/F2maize_geno.txt';\ MKSCORES=mkscores; MKNAMES=mknames; IDMGENOTYPES=idmgeno;\ PARENTS=parents GROUPS mknames; FACTOR=markers QRECOMBINATIONS [POPULATION=F2; METHOD=twopoint; TITLE='F2 maize']\ MKSCORES=mkscores; MKNAMES=mknames; RECFREQUENCIES=recfreq;\ PARENTS=parents QMKSELECT [PRINT=MONITORING,SUMMARY; NCLUSTERS=10; METHOD=sampling]\ MKNAMES=mknames; RECFREQUENCIES=recfreq;\ SELECTED=SELECTED; NEIGHBOURS=NN; DISTANCES=DISTNN;\ SEED=12345