Recodes marker scores into separate alleles (L.C.P. Keizer & J.T.N.M. Thissen).
Options
PRINT = string tokens |
What to print (alleles, summary); default alle |
|---|---|
POPULATIONTYPE = string token |
Type of population (BC1, DH1, F2, RIL, BCxSy, CP, AMP); must be set |
MISSING = text |
Character representing a missing genotype; default '-‘ |
USEFIRSTGENOTYPE = string token |
Makes all the first (and second) labels of the LABALLELES pointer from the first genotype of the population (yes, no); default no |
ASEPARATOR = text |
Character separating allele values; default '/' |
Parameters
MKSCORES = pointers |
Marker scores; must be set |
|---|---|
MKALLELES = pointers |
Saves the marker scores per allele |
LABALLELES = pointers |
Saves the allele labels |
MKLABALLELES = pointers |
Saves the allele labels per marker |
NALLELES = variates |
Saves the number of alleles per marker |
MKNAMES = texts |
Names of the markers |
Description
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 LABALLELES parameter.
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 MKSCORES pointer). 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 ASEPARATOR option.
The PRINT option controls the printed output, with settings:
| alleles | for details of the alleles, and |
|---|---|
summary |
for a general summary. |
By default PRINT=alleles.
Options: PRINT, POPULATIONTYPE, MISSING, ASEPARATOR.
Parameters: MKSCORES, MKALLELES, LABALLELES, MKLABALLELES, NALLELES, MKNAMES.
Action with RESTRICT
Restrictions are not allowed.
See also
Procedure: QMKDIAGNOSTICS.
Commands for: Statistical genetics and QTL estimation.
Example
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[1][]; DECIMALS=0
PRINT al[6][]; DECIMALS=0
PRINT al[13][]; DECIMALS=0
PRINT mknames,nalleles; DECIMALS=0