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QCANDIDATES procedure

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
Updated on March 6, 2019

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