Only TSV format is allowed.
Only TSV format is allowed.
When uploading the dataset, LAVAA expects to find the columns with the matching headers as described in the following table.
You can download a sample file to use as a template for your own data. With this file you can also edit out or add in phenotypes and change the labels for presentation and publication. Note that the file must be in TSV (tab-separated value) format.
| Name | Column | Required | Description |
|---|---|---|---|
| Phenotype name | phenostring | Yes | A string describing the phenotype. |
| Phenotype code | phenocode | No | A shorthand code describing the phenotype. |
| ICD category | category | No | In FinnGen data categories are chapters in the ICD-10 hierarchy, however, you can introduce your own categories as well. This enables you to color all conditions affecting a certain organ system or type of disease (cancer, infection, etc) with the same color for the points. Additionally, convex hulls (see below) can show you where all of these points of one category exist. |
| P-value | pval | Yes | The P-value for the associated phenotype. |
| Beta | beta | Yes | The effect size of the genetic association. |
| Cases | n_case | No | Number of cases of the phenotype. |
| Controls | n_control | No | Number of controls of the phenotype. |
| PIP | pip | No | The Posterior Inclusion Probability is an optional measure from 0 to 1 that is a result of fine-mapping. It indicates which variants in a region are in a credible set. |
Datapoint selection
Brush through the data points by drawing a rectangle anywhere on the chart to see a table of details about the data. You can reset the brush by clicking anywhere on the chart. To clear the detailed data, press ‘clear selection’.
Filtering with categories
You can highlight data points in a phenotypic category by hovering over the legend next to the chart. For instance, you might want to see all the phenotypes relating to The legend represents the categories of data above the significance line. FinnGen ICD-based categories are displayed but your own categories can be used also.
Zooming
Inspect your own selection by drawing a rectangle anywhere on the chart and pressing enter.
Marking the points
Mark interesting data points by clicking on them and move the label around by dragging it. Remove individual labels by clicking on a close -button that appears on hover, or reset all labels by double-clicking a point.
Significance threshold
A line at 5.8 x 10-8 indicates the threshold for genomewide significant results.
Category hulls
A convex hull is the smallest convex polygon containing a set of points on a grid. In LAVAA they are used to connect all the data points that are in a particular category of associations, showing its extent on the chart. Convex hulls can help draw your eye to where the points in a certain category fall (e.g. are they the same direction of effect) and also to see if some are perhaps just below the significance threshold.