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QREPORT procedure

Creates an HTML report from QTL linkage or association analysis results (D.A. Murray).


OUTFILEPREFIX = text Prefix to use for the files that are generated
WORKDIRECTORY = text Working directory to use for files; default current Genstat working directory
CHROMOSOMES = factor Factor defining linkage groups for the genetic map
POSITIONS = variate Positions of markers within the linkage groups for the genetic map
HTMLHEAD = text Text structure containing custom content for the header of the HTML report file


QSAVE = pointers Information and results saved from an earlier QTL analysis


QREPORT creates an HTML report containing results from QTL linkage or association analyses. The QSAVE parameter of the QSESTIMATE, QMESTIMATE, QSASSOCIATION and QMASSOCIATION procedures can be used to save a pointer containing information and results for the significant QTLs. You can then produce an HTML report of the results, by using this pointer as the setting of the QSAVE parameter of QREPORT. If you specify a list of pointers, these will all be collated into a single report.

The OUTFILEPREFIX option specifies the name to use as the prefix for the file and associated graphs. The HTML report file is created using the prefix string with the extension .htm appended to the name. All graphs produced in the report are produced in PNG format using the prefix string in their file name. The files are saved within the working directory, which by default will be the current directory. However, an alternative directory can be supplied using the WORKDIRECTORY option.

A genetic map indicating the location of the significant QTLs can be included within the report, by supplying the linkage groupings and positions within the linkage groups, using the CHROMOSOMES and POSITIONS option, respectively.

The HTMLHEAD option allows you to supply additional markup content for the document header of the HTML file, which will be inserted between the and tags. It can be set either to a text containing all the HTML markup, or to the name of a file containing that information. It is intended primarily for inserting CSS style information; for more details see the OPEN directive. If HTMLHEAD is not set, QREPORT inserts the content of the file Genstat.css, which is supplied in the Source directory of the Genstat installation. This defines a number of classes that are used at various points in the Genstat output (for example to define styles used for output from the CAPTION directive). The file can be used as a template from which to derive a local variation, redefining basic elements of output.


Parameter: QSAVE.


The HTML report is produced by writing to an output file, opened by the OPEN directive, with parameter STYLE=html. The graphs are inserted in the report using the PLINK procedure.

Action with RESTRICT

Any data restrictions are ignored.

See also

Directive: OPEN.


Commands for: Statistical genetics and QTL estimation.


CAPTION    'QREPORT example'; STYLE=meta
SPLOAD     [PRINT=*] '%GENDIR%/Examples/F2maize_traits.gsh'
&          '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='LOCI'
&          '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='ADDPREDICTORS'
QIMPORT    [POPULATION=f2] '%GENDIR%/Examples/F2maize_geno.txt';\
           MAPFILE='%GENDIR%/Examples/F2maize_map.txt'; CHROMOSOME=chr;\
" Create a single environment "
SUBSET     [E.EQ.6] G,yld
" Canditate QTL positions from QSBACKSELECT "
VARIATE    [VALUES=19,111,237] Qid
           TRAIT=yld; GENOTYPES=G; CHROMOSOMES=mkchr; POSITIONS=mkpos;\
           IDLOCI=idlocus; MKLOCI=marker; ADDITIVEPREDICTORS=addpred;\
           QTLSELECTED=Qid; QEFFECTS=qeff; QSE=qse;\
Updated on June 19, 2019

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