Replaces missing marker scores with the mode scores of the most similar genotypes (L.C.P. Keizer, J.T.N.M. Thissen & F.A. van Eeuwijk).
|What to print (
||Number of nearest neighbours; default 5|
||Maximum similarity difference; default 0.1|
||Pointer with the original marker scores; must be set|
||Labels for genotypes|
||Pointer to store the new marker scores; must be set|
QMVREPLACE replaces missing marker scores with the mode score of the most similar genotype(s). The marker scores with missing values are supplied by the
MKSCORES pointer, which contains a factor for each marker. The length of factors is the number of genotypes. The new factors, in which the missing marker scores are replaced, can be saved by the
NEWMKSCORES pointer. The
IDMGENOTYPES parameters can be set to obtain more readable output.
QMVREPLACE forms a similarity matrix from the marker scores using the
FSIMILARITY directive with parameter
NNEIGHBOURS option specifies the number of most-similar neighbouring genotypes to use when filling in the missing values for each genotype (default 5). To prevent the use of neighbours that are too different from the genotype, neighbours are selected only if their distances from the genotype are less than the value supplied by the
MAXDISTANCE option (default 0.1). For each missing marker score of the genotype, a replacement value is obtained by taking the score that is most common amongst the selected neighbouring genotypes (i.e. the mode of their values). If the marker scores of the closest genotypes are all missing, the missing value is not replaced.
||prints general information about the replaced marker missing scores,|
||prints the similarity matrix,|
||prints the most-similar neighbours of the genotypes with missing marker scores, and|
||prints information about each replacement,|
Restrictions are not allowed.
Commands for: Statistical genetics and QTL estimation.
CAPTION 'QMVREPLACE example'; STYLE=meta QIMPORT [POPULATION=amp] '%GENDIR%/Examples/Qassociation_geno.txt';\ MAPFILE='%GENDIR%/Examples/Qassociation_map.txt';\ MKSCORES=scores; CHROMOSOMES=mkchr; POSITIONS=mkpos; MKNAMES=mknames QMVREPLACE [PRINT=summary] scores; NEWMKSCORES=mkout