xQTL workbench - Tutorial for biologists: Uploading a new dataset
We will start by uploading a dataset with geno- and phenotype information. There are many ways to enter data into xQTL, such as uploading CSV or Excel files, using the R API, or manual per-record entry. To make uploading a typical QTL-study dataset as easy as possible, we developed a specialized 'R/qtl importer'. Note: for more general information about uploading data, see: xQTLBiologistImport
Step 1: Download example data
Let's first download an example dataset that is accepted by this importer. Download the respective genotype, phenotype and map files from:
Yeast_genotypes
Yeast_phenotypes
Yeast_map
Step 2: Inspect example data
If you open these files, you will see that the format is very straightforward. Some things to keep in mind:
- For the R/qtl importer, the individuals of the set MUST be on the first line in both files, to form the 'column headers'.
- Some values and headers are between quotation marks: this is not mandatory but it can help xQTL to read CSV files.
- The value seperator is tab, but others such as whitespace or comma are also recognized.
- The genotype values are 1, 2 and NA. Typically NA values are coded simply as empty strings (so no character between two seperators), and genotypes as A, B, AB / H. In this case the NA's will be parsed by R to empty, and the real genotypes estimated from frequency and cross type.
You can ofcourse also use your own data if the format is good enough.
Step 3: Upload data into system
Now let's import them. Go to Upload data, R/qtl in the main menu.
Under Genotypes:
- Click Browse and select your genotype file.
- In the dropdown for cross type, select xgap_rqtl_straintype_riself. This will cause xQTL to automatically add the needed annotations for Individuals (if they are not yet) to the database, with a certain cross type linked to them. This is important because R/qtl needs to know what kind of population structure it's dealing with.
- Press Upload.
Under Phenotypes::
- Click Browse and select your phenotype file.
- In the dropdown for traits, select the type of traits you are uploading. In this case: Probe. This will cause xQTL to automatically add the needed annotations for these traits to the database. In an ideal situation you never want to do this, because traits such as Probe should always come annotated with basepair location, gene linkouts, etc. When automatically added, we only assign a name to the traits, and you should update the annotations later on manually.
- Press Upload.
Under Map::
- Click Browse and select your phenotype file.
- When uploading, missing marker and chromosome annotations are added to the database based on this file.
- Press Upload.
There should be a green success message after each uploaded file. If not, you must adjust the formatting of your files, are maybe cleanup the database, it depends on the message.
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