Open Marker and Map Data Files
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This dialog can be used to import marker scores and associated map data for QTL analysis. When data are imported they can be added to the QTL workbook for use within the QTL menus.

Select file type

The lists the different file types that data can be imported from. Data can be imported from R/QTL comma delimited text files (.csv) and MapQTL locus genotype and map files (.loc, .map). Data from other file types can be imported using the File | Open menu item, however the structure names will not be added to the QTL workbook automatically athough this can be done manually using the view workbook dialog.

LOC Filename

When importing data from MapQTL locus genotype and map files this specifies the name for the locus genotype data file. This file contains the information for the type of population and the genotype scores for each locus. You can browse for a filename by clicking on the button.

MAP Filename

When importing data from MapQTL locus genotype and map files this specifies the name for the map data file. This file contains the map positions and linkage group information for all loci. You can browse for a filename by clicking on the button.

CSV Filename

When importing data from R/QTL comma delimited text files this specifies the marker scores, map positions and linkage groups. The .csv file format uses an extended version of the R/QTL rotated comma-delimited separate file for genotype data (csvsr), where there is an optional column for marker sets. In the .csv file the first row specifies the genotype id, and for a QTL analysis these genotype id labels should match the labels for the phenotypic genotype factor associated with the trait means. The first cell should be the name of an identifier for the genotype id, and the first row in columns 2 and 3 should be blank. Also, if marker sets are included in the file, the first row of column 4 should be left blank. Starting from row 2 in the file, the first column gives the marker names, the second column gives the linkage group for each marker, and the third column gives the positions of the markers within the linkage groups. The fourth column can be used to contain the marker sets. The remaining columns give the marker genotype scores. You can browse for a filename by clicking on the button.

Save data in

Specifies the data structure names to save the data in.
Marker genotypespointerCreates a pointer containing a set of factors (one for each marker) where each factor has the same labels representing the genotype scores and the labels are all in the same order.
Marker namestextCreates a text containing the marker names.
Linkage groupsfactorCreates a factor identifying the linkage group for each marker.
Positions within linkage groupsvariateCreates a variate containing the positions within the linkage groups for each marker.
Genotype labelstextCreates a text containing id labels for genotypes. These can be used to ensure the genotypes for the phenotypic data matches the map data.

Add data to QTL workbook

When selected the imported data structure names will be added to the QTL workbook so that the names of the structures will be present in the QTL menus.

Action Buttons

OpenImports the data and closes the dialog.
CancelClose the dialog without making any changes.

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