To support running GO-PCA with custom gene sets ("GS-PCA"), GO-PCA can be given only a GO annotation file (-a parameter) and no ontology file (-t parameter). In this case, GO-PCA's "global filter" (filtering against related gene sets found to be enriched among previously analyzed principal components) cannot rely on the GO hierarchy (the custom gene sets do not represent GO terms).
Currently, when no ontology file is provided, the "global filter" is automatically disabled. However, even if there is no known relationship between the custom gene sets provided, we can at least prevent the same gene set from generating multiple signatures. This should be the default behavior, and the current behavior should only occur when the global filter is explicitly disabled by the user.
To support running GO-PCA with custom gene sets ("GS-PCA"), GO-PCA can be given only a GO annotation file (
-aparameter) and no ontology file (-tparameter). In this case, GO-PCA's "global filter" (filtering against related gene sets found to be enriched among previously analyzed principal components) cannot rely on the GO hierarchy (the custom gene sets do not represent GO terms).Currently, when no ontology file is provided, the "global filter" is automatically disabled. However, even if there is no known relationship between the custom gene sets provided, we can at least prevent the same gene set from generating multiple signatures. This should be the default behavior, and the current behavior should only occur when the global filter is explicitly disabled by the user.