Predictive Ability

This guide provides a comprehensive walkthrough for utilizing the Predictive Ability feature in the BIGapp. It outlines the process of uploading files, selecting traits, and running analyses, while also highlighting advanced options for more tailored results.

Alex Sandercock
23 steps
3 minutes

Genomic Selection is broken down into two separate modules. This module, Predictive Ability, is used to estimate the "predictive ability" for selected trait(s). The predictive ability is the pearson correlation between the predicted trait and the user supplied trait. BIGapp uses a 5-fold cross-validation summarized across the user defined number of iterations to estimate the predictive ability values.

On the left hand side menu, choose "predictive ability".

Predictive ability option on the left hand menu highlighted

Under "choose VCF file", select "browse" and select your file.

Under choose VCF file, "browse" highlighted

Once your file is selected, click "open".

Choose "browse" under the trait file heading.

Browse highlighted under choose trait file heading

Select your file and then click "open".

Select the species ploidy.

Select species ploidy selection highlighted

Select the iterations you wish to have.

Change iterations increase or decrease selection highlighted

Make your trait selection. You may choose more than one.

Select traits with sepal width highlighted

Select your fixed effects.\ Please note that this is a beta feature.

Optional beta select fixed effects option highlighted

Find summary and example file information here.

Yellow informational box with summary, parameters information, and example files

Advanced options are available for analysis. To select, click on "advanced options".\ Please note that this is a beta feature.

Advanced options selection highlighted (beta feature)

Select your method and relationship matrix choice and then click "save".

Relationship matrix choice with GMatrix highlighted

Please note that additional information may be needed.\ In this example, a Hmatrix relationship matrix choice requires the upload of a pedigree file.\ When you are satisfied with your selections, click save. If you are not satisfied, you can change your selections, or click close.

Select "run analysis".

View your results. Notice that the various results can be viewed by clicking on the various tabs.\ This is the Violin Plot.

Box plot example

P.A. Table example

Plot controls are available on the right hand side of the screen. To change color, select the small arrow.

Choose your new color.

Note that the box plots are now in the new color selection.

You can view additional information in the upper right hand screen corner such as the number of SNPs and number of samples with phenotype information.

Number of SNPs in genotype file box highlighted

Save images by clicking on the red "save" button.

Select the figure, file type, resolution, width and height that you wish for your image. You can then save the image or you can save the file by selecting the appropriate grey box at the bottom.

You have completed this training module for Predictive Ability in the BIGapp. Return to the main training page to learn more about other BIGapp features.