[[TracNav(xQTL)]]

= [wiki: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.