Recodes marker scores into separate alleles (L.C.P. Keizer & J.T.N.M. Thissen).
|What to print (
||Type of population (
||Character representing a missing genotype; default
||Makes all the first (and second) labels of the
||Character separating allele values; default
||Marker scores; must be set|
||Saves the marker scores per allele|
||Saves the allele labels|
||Saves the allele labels per marker|
||Saves the number of alleles per marker|
||Names of the markers|
QMKRECODE recodes the marker scores, specified by the
MKSCORES parameter, into separate alleles. These separate alleles can be saved by the
MKALLELES parameter, in a pointer with two levels of suffixes. The first level has an element for each marker names; the second level has as many elements as the number of alleles of the marker. The labels of the alleles per marker can be saved with the
If you set option
USEFIRSTGENOTYPE=yes, all the first
LABALLELES correspond to the first individual in the
MKSCORES pointer (for association analysis). The number of the alleles per marker can be saved by the
NALLELES, and the names of the markers by the
MKNAMES parameter (from the labels of the
MKLABALLELES is similar to the
LABALLELELS but inverted. So it is not a pointer for alleles per marker (with elements of unequal length). Instead it is a pointer that contains the first up to maximum number of alleles for all markers, and missing positions where there were less alleles. This may be more convenient for printing and reporting.
The type of population must specified using the
POPULATIONTYPE option. The
MISSING option specifies a character to identify missing genotypes (default
'-'). Genstat expects the alleles for each genotype to be separated using a
'/' character, but an alternative can be supplied using the
|alleles||for details of the alleles, and|
||for a general summary.|
Restrictions are not allowed.
Commands for: Statistical genetics and QTL estimation.
CAPTION 'QMKRECODE example'; STYLE=meta QIMPORT [POPULATION=amp]\ FILENAME='%GENDIR%/Examples/Qmkrecode_geno.txt';\ MKSCORES=scores; MKNAMES=markers QMKRECODE [PRINT=summ,all] scores; MKALLELES=al; LABALLELES=labels;\ NALLELES=nalleles; MKNAMES=mknames PRINT scores[1,6,13] PRINT labels[1,6,13] PRINT al; DECIMALS=0 PRINT al; DECIMALS=0 PRINT al; DECIMALS=0 PRINT mknames,nalleles; DECIMALS=0