A small tool that will help you visualize the GWAS results from many different experiments. You can cite the SNPer as: Julkowska, M.M. “V1.0.2 mmjulkowska/SNPer: Release including README :)” DOI: 10.5281/zenodo.1227775
you can either run the SNPer on-line or by typing into the terminal windown of the R/S-studio the following commands:
The accepted data format is “.csv” files.
In the first tab - select your file and select all the neccessary column identifiers from the drop-down menus. Once you are finished, click on “Set the dataset” button.
The new dataset can be viewed in the sub-tab “Selected data”
In the tab “SNP-viewer” you can select whichever traits you want to view (unlimited number) and the chromosome.
After selecting all - click on “Unleash SNPer” button. You can change the transparency of the dots by changing the value in the “transparency box” below 1.
You can also zoom in into the graph by selecting the zoom-in region.
To zoom out click “autoscale” button within the graph.
In order to get the information about the exact position of the associated SNP, put your cursor over the specific SNP.
If you change the chromosome, make sure to agan press “Unleash SNPer” to update the graph.
Happy Forward Genetic analysis!