TracNav(xQTL)?

xQTL workbench - Import new data

Geno- and phenotypic data

• A special importer for R/qtl data is available under the tab Upload data.
• First, choose the Investigation where you want to upload into.
• Select a geno, pheno or map file in the corresponding location and press Upload.
• Repeat this process to upload more data.

Please note:

• The filename is used as data matrix name. Choose it carefully.
• The created data matrices are tagged as Rqtl analysis pheno or geno datasets. They will appear when running a default QTL analysis.
• When uploading a map file, marker and chromosome annotations are created in the database.
• Individual and trait (phenotype) annotations are also automatically created if they don't exist.
• Pay attention to the drop down boxes for cross type (for missing Individuals) and data type (for missing traits) before pressing upload.
• Different seperators are recognized in all file uploads. Usual ones include tab, whitespace or comma.

Help: my QTL analysis fails!

Please check the following:

• The markers in the genotype matrix must be annotated in the map file. The names must exactly match. Check use the Inspect tool in Data matrices to verify data consistency. You can always manually add or manipulate markers at any point using View annotations, click Markers.
• For a correct new data set, the exact same individual names must be used in the genotype and phenotype file.
• The QTL analysis needs to know which type of cross was used. It looks at the annotation of the first individual of the genotypes to get cross type from the ontologyReference field. Set this to e.g. xgap_rqtl_straintype_riself to indicate the cross is a recombinant inbred line by selfing. The coding is taken from Rqtl.

Help: my individuals are not on the first line!

The importers for genotype and phenotype files expect you to put individuals on the first line, making them the column headers. If your rows and columns are 'flipped' and would need transposing, don't worry. Just upload the files. You should just re-annotate your rows and columns by going to Browse data in the main menu, then select View data and find your recent uploaded data matrix. Click Show additional fields to show the full annotation. Use the dropdown menus to swap the values of FeatureType (columns) and TargetType (rows). Press save the changes. BEWARE: if you let xQTL automatically add individuals, markers, and/or traits, you might end up with your markers being added as Individuals and vice versa. If you choose to upload and 'transpose' the dataset, add your annotations first.

Other data

Annotations:

• Annotation data should be added using the Add new record button in the corresponding subtab of View annotations of your choosing.
• Alternatively, you can perform a CSV file batch upload in the menu File, or upload data via the R api.

Data matrices:

• Matrix data can be added by creating a new Data record in the Data matrices tab.
• The View plugin will inform you there is no data linked to this entry, and you can upload it via direct CSV input or file.

Excel:

• You can upload a multitude of different annotations in a convenient Excel file to xQTL using this import wizard.
• Select your Excel file (at the moment, only *.xls is supported) and press Upload.
• Review the consistency of your dataset in the following Import prognosis screen.
• If you are satisfied with the predictions, press Import.

Plink:

• The Plink importer lets you upload several Plink files at once under a new, common name.
• The files are simply put into the database as is, and you can find them back under the Files tab in the same menu.
• In addition to the upload and rename step, the files are tagged as input for the example Plink analysis.
• You can find these tags in the Configure analysis menu, Parameters tab, Plink_params entry.

Other files:

• In the Files tab, you can upload any file you like. Files belong to an investigation.
• Click the Add new record button. In the popup, fill in a file name, extension and investigation. For example MyPicture, png, and selecting ClusterDemo.
• This record will be the link to the actual file. You can upload it in the box below, or type some text and upload that as a text data file.
• When removing the record, you also removed the associated file.
• Remember that files can be uploaded and downloaded programmatically via the /downloadfile and /uploadfile webservices.