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QFLAPJACK procedure

Creates a Flapjack project file from genotypic and phenotypic data (D.A. Murray).


WORKDIRECTORY = text Working directory to use for files; default current Genstat working directory
FJPATH = text Path specifying the location of Flapjack; by default QFLAPJACK searches for a version of Flapjack installed within C:\program files (x86)\Flapjack or C:\program files\Flapjack
DECIMALSYMBOL = string token Controls whether to use the locale (automatic) or English (dot) representation of decimal marks (automatic, dot); default auto


FJFILENAME = texts Name of the Flapjack project file to create
TRAITS = pointers Pointer to variates containing the phenotypic trait data
GENOTYPES = factors Genotype factor associated with the traits
ENVIRONMENTS = factors Environment factor
GENFILENAME = texts Name of a Flapjack genotype file
MAPFILENAME = texts Name of a Flapjack map file
FJTRAITFILENAME = texts Name of a file to supply the trait data, or to save them if the TRAITS and GENOTYPES parameters are also set
FJQTLFILENAME = texts Name of a file to supply the QTL results, or to save them if the QSAVE parameter is also set
QSAVE = pointers Information and results saved from an earlier QTL analysis


Flapjack is a tool for graphical genotyping and haplotype visualization that can routinely handle the large data volumes generated by high throughput SNP and comparable genotyping technologies. Its visualizations are rendered in real-time allowing for rapid navigation and comparisons between lines, markers and chromosomes. QFLAPJACK can be used to create a Flapjack project file containing genotypic and phenotypic data along with QTL results. The name of the Flapjack project file is specified by the FJFILENAME parameter.

To use QFLAPJACK, the Flapjack software must be installed on the current system. The location of the Flapjack to use to create the project file is specified using the FJPATH option. If FJPATH is not specified, QFLAPJACK searches for a version of Flapjack installed within the directories

C:\program files (x86)\Flapjack


C:\program files\Flapjack

The genotypic marker and map data must be supplied in Flapjack genotype and map text files. The name of the genotype file is specified using the GENFILENAME parameter, and the name of the map file is specified using the MAPFILENAME parameter. These files can be created from Genstat data structures using the QEXPORT procedure.

Phenotypic data can be added to the project file from a text file whose the name is specified by the FJTRAITFILENAME parameter. The data within the file should be tab separated, with the first column containing the genotype labels, and the remaining columns containing the traits. Alternatively, you can use the TRAITS parameter to supply the trait data, in a pointer to a set of variates, and the GENOTYPES parameter to supply the associated genotype factor. For multi-environment trials, you should also use the ENVIRONMENTS parameter to supply a factor to identify the environments. If you specify FJTRAITFILENAME as well as TRAITS and GENOTYPES, the phenotypic data will be saved in the file whose name is specified by FJTRAITFILENAME; this can then be used in a later QFLAPJACK command.

The results from a QTL analysis can be included within the Flapjack project file by using the FJQTLFILENAME parameter to supply a text file containing the results. Details of the file layout for importing supplementary QTL data within a Flapjack project are given within the Flapjack application. Alternatively, the QSESTIMATE and QMESTIMATE procedures allow you to save results from a linkage analysis in a pointer, using their QSAVE parameters. This can then be used as the setting of the QSAVE parameter of QFLAPJACK to supply the QTL data. If you specify FJQTLFILENAME as well as QSAVE, the QTL data will be saved in the file whose name is specified by FJQTLFILENAME; this can then be used in a later QFLAPJACK command.

By default, the working directory will be the current directory. However, an alternative directory can be supplied using the WORKDIRECTORY option.

The DECIMALSYMBOL option controls the type of decimal marks to use in the Flapjack project file, with the following settings:

    automatic uses the locale settings, and
    dot uses the English-style dot (.).




In Windows the project file is formed using the Createproject.exe executable within the Flapjack installation. A bat file containing the command line to form the project file is created, and then executed using the SUSPEND directive.

Action with RESTRICT

Any data restrictions are ignored.

See also

Directive: SUSPEND.


Commands for: Statistical genetics and QTL estimation.


CAPTION    'QFLAPJACK example'; STYLE=meta
SPLOAD     [PRINT=*] '%GENDIR%/Examples/F2maize_traits.gsh'
&          '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='LOCI'
&          '%GENDIR%/Examples/F2maizemarkers.GWB'; SHEET='ADDPREDICTORS'
" Create a single environment "
SUBSET     [E.EQ.6] G,yld
" Candidate QTL positions from QSBACKSELECT "
VARIATE    [VALUES=19,111,237] Qid
QSESTIMATE [PRINT=summary,model,wald,effects; POPULATIONTYPE=F2]\
           TRAIT=yld; GENOTYPES=G; CHROMOSOMES=mkchr; POSITIONS=mkpos;\
           IDLOCI=idlocus; MKLOCI=marker; ADDITIVEPREDICTORS=addpred;\
           QTLSELECTED=Qid; QEFFECTS=qeff; QSE=qse; QSAVE=Output
QFLAPJACK  'F2maize.flapjack'; TRAITS=!p(yld); GENOTYPES=G;\
	         MAPFILENAME='%GENDIR%/Examples/F2maize_map.txt'; QSAVE=Output
Updated on June 19, 2019

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