NEWS
categoryCompare2 0.200.9
- added more tests to up the test coverage, and a test coverage badge.
categoryCompare2 0.200.8
- fixes a long standing non-standard evaluation bug where if you tried to use an argument in a filtering operation, it would fail if it was within another function, or run in another process (#29).
categoryCompare2 0.200.7
- fixes a bug where setting significant annotations where there was only a single enriched object in the combined object would return zero counts for enriched, which is not correct. Added test to verify the fix (#52).
- fixes testing bugs where numbers of things would change due to changes in GO.db or the entrez annotation packages (#53).
categoryCompare2 0.200.6
- implements a method for getting a statistical table for a single
enriched_result.
categoryCompare2 0.200.5
- fixes getting statistics from
gsea results, and actually has a test that it works.
categoryCompare2 0.200.4
- fixes exporting annotation objects to JSON, in that every item should consistently be in a list array, and not a bare string when there is only a single annotated item.
categoryCompare2 0.200.3
- adds the
hypergeometric_features, gsea_features and binomial_features constructors as functions to make it easier to remember the arguments for the actual classes of the same names (#49).
categoryCompare2 0.200.2
- changes
hypergeom_features to hypergeometric_features.
- because the
hypergeometrc_features necessitates changes to actual code written by any users, I bumped the version from 0.100 to 0.200.
- implements
hypergeometric_result, gsea_result, and binomial_result as more specific classes of enrichemnt_result, which makes all of the combining and filtering work for everything.
- made the vignettes use pre-processed data so that there won't be any issues from the
affy package and segfaults (#50).
categoryCompare2 0.100.32
- changes
binomial_feature_enrichment min_features to 6, as anything under this is not likely to be useful for binomial testing.
- fixes some failing tests.
- adds ability to use
combine_enrichments on binomial_enriched objects.
categoryCompare2 0.100.31
- changes to
gocats_2_annotation, checking for GO terms with no description, the actual base GO terms for each portion, and adding min and max arguments for the number of features annotated to a term.
categoryCompare2 0.100.30
- adds documentation in the CLI vignette to using GSEA on the command line.
- fixes
filter_and_group.R to allow filtering of CLI GSEA results.
- adds documentation in the CLI vignette about the JSON structure of each of the input files, both for hypergeometric testing and GSEA.
categoryCompare2 0.100.28
- adds gene-set enrichment analysis (GSEA) to the command line interface. Note that this is only available by running
run_enrichment.R directly. Currently, there is no way to modify the GSEA options, such as min_n and max_n.
categoryCompare2 0.100.25
- adds gene-set enrichment analysis (GSEA) using the
fgsea package. See gsea_features and gsea_feature_enrichment.
categoryCompare2 0.100.22
- Fixed a bug where if nothing was significant, then all annotations were pulled into the graph.
categoryCompare2 0.100.21
- Added more output in the binomial testing.
categoryCompare2 0.100.16
- Fixing bugs around binomial testing.
categoryCompare2 0.100.9
- Better importing of gocats objects.
categoryCompare2 0.100.8
- Made it possible to do iterative filtering and grouping of the graph in the CLI.
categoryCompare2 0.100.7
categoryCompare2 0.100.1
- P-value adjustment is done by default.
categoryCompare2 0.99.161
categoryCompare2 0.99.160
- Document finding communities in the vignettes.
categoryCompare2 0.99.159
- CLI executables are available.
categoryCompare2 0.99.129
- Really became the try inheritor to the original categoryCompare.