Selects QTLs on the basis of a test statistic profile along the genome (M.P. Boer & J.T.N.M. Thissen).
|What to print (
||Threshold for the test statistic; default 0|
||Minimum distance in cM between two peaks to be selected as two QTLs; default 10|
||Test statistic along the genome; must be set|
||Chromosome for each locus; must be set|
||Position on the chromosome for each locus; must be set|
||Labels for the loci|
||Saves the index numbers of the selected QTLs|
QCANDIDATES selects the peaks in the test statistic profile along the genome. These profiles, calculated with the procedures
QMQTLSCAN, must be supplied by the
STATISTICS parameter. Information about chromosome number and position on the chromosome must be provided by the
POSITIONS parameters respectively. Names to identify the loci can be specified using the
The selection depends on the
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.
Restrictions are not allowed.
Commands for: Statistical genetics and QTL estimation.
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