Selects QTLs on the basis of a test statistic profile along the genome (M.P. Boer & J.T.N.M. Thissen).
Options
PRINT = string token |
What to print (summary); default summ |
|---|---|
THRESHOLD = scalar |
Threshold for the test statistic; default 0 |
QTLWINDOW = scalar |
Minimum distance in cM between two peaks to be selected as two QTLs; default 10 |
Parameters
STATISTICS = variates |
Test statistic along the genome; must be set |
|---|---|
CHROMOSOMES = factors |
Chromosome for each locus; must be set |
POSITIONS = variates |
Position on the chromosome for each locus; must be set |
IDLOCI = texts |
Labels for the loci |
QTLCANDIDATES = variates |
Saves the index numbers of the selected QTLs |
Description
QCANDIDATES selects the peaks in the test statistic profile along the genome. These profiles, calculated with the procedures QSQTLSCAN or QMQTLSCAN, must be supplied by the STATISTICS parameter. Information about chromosome number and position on the chromosome must be provided by the CHROMOSOMES and POSITIONS parameters respectively. Names to identify the loci can be specified using the IDLOCI parameter.
The selection depends on the THRESHOLD and SEPARATION options. Positions with a STATISTICS score greater than THRESHOLD are eligible for selection. The maximum STATISTICS score along the genome is selected as the first QTL. Then futher STATISTICS scores are selected, one at a time, at each stage taking the maximum score of those with a distance of at least QTLWINDOW from the QTLs that have already been selected. The search continues until no further statistics scores are found above THRESHOLD and with a distance of QTLWINDOW or more from the other selected QTLs.
Options: PRINT, THRESHOLD, QTLWINDOW.
Parameters: STATISTICS, CHROMOSOMES, POSITIONS, IDLOCI, QTLCANDIDATES.
Action with RESTRICT
Restrictions are not allowed.
See also
Procedures: QMQTLSCAN, QSQTLSCAN.
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QCANDIDATES example'; STYLE=meta
SPLOAD '%GENDIR%/Examples/F2maizemarkers.gwb'; SHEET='LOCI'
SPLOAD '%GENDIR%/Examples/F2maize_multi_out.gwb'
SCALAR thres; VALUE=3.16 "from QMQTLSCAN"
QCANDIDATES [PRINT=summary; QTLWINDOW=1; THRESHOLD=thres]\
CHROMOSOMES=mkchr; POSITIONS=mkpos;\
IDLOCI=idlocus; STATISTICS=minlog10p; QTLCANDIDATES=qtls
QCANDIDATES [PRINT=summary; QTLWINDOW=100; THRESHOLD=thres]\
CHROMOSOMES=mkchr; POSITIONS=mkpos; IDLOCI=idlocus;\
STATISTICS=minlog10p; QTLCANDIDATES=qtls