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NEWS
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NEWS
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CHANGES IN VERSION 1.6.0
------------------------
o [Bug Fix]
- `PCAGenomicSignatures` construction function has a bug in its object
inheritence step, which is fixed now.
- `validate` function can perform better with scRNAseq data, because it now
uses `irlba` instead of `prcomp`, which significantly improves the speed.
o [Major]
- `rowNorm` function is deprecated.
- Remove the `scale` argument of `validate` function.
- Deprecate the `rowNorm` function.
o [Minor]
- Citation is added.
CHANGES IN VERSION 1.4.0
------------------------
o [Bug Fix]
- `findStudiesInCluster`: single-element clusters return the correct
study now, instead of `null`
o [Major]
- `findStudiesInCluster`: the output includes PC number of the participating
study in the cluster and the variance explained by them. With `studyTitle=FALSE`,
the output will be a data frame, not a character vector.
- `subsetEnrichedPathways`: the new argument `include_nes` is added. If it
is set to `TRUE`, the output will include NES from GSEA.
- `getRAVInfo` and `getStudyInfo`: two new functions to extract basic
metadata for RAVs and studies, respectively.
- We characterize RAVs that are harder to interpret with the currently available
information associated with them (more detail can be found bit.ly/RAVmodel_characterization).
For the following functions, any output including those RAVs will have a
defulat message: `meshTable`, `drawWordcloud`, `heatmapTable`, `validatedSignatures`.
You can snooze this by setting `filterMessage = FALSE`
- New required parameter `RAVmodel` for the following functions:
`annotatePC`,`heatmapTable` and `validatedSignatures`.
- New accessor `version` is available to check the version of RAVmodel
- New function `availableRAVmodel` will output the different versions of
RAVmodels available for downloading now.
- `getModel` function now takes a new argument, `version`, to specify the
version of RAVmodel to download.
o [Minor]
- miniRAVmodel is updated
CHANGES IN VERSION 1.2.0
------------------------
o [Bug Fix]
- `n` argument of `annotatePC` was hard-coded. Now it can return
different number of enriched pathways.
- `abs` argument of `annotatePC` was fixed.
- Fix wrongfully assigned variable within `plotAnnotatedPCA` function.
o [Major]
- `drawWordcloud` has a new argument `droplist`.
- Argument name for `plotAnnotatedPCA` is changed from `PCs` to `PCnum`.
- New argument `studyTitle` for `findStudiesInCluster` function.
o [Minor]
- Description of the package is updated.
- If non-existing index is provided for any function, it will return with
the error message.
CHANGES IN VERSION 1.0.0
------------------------
o Initial release of the 'GenomicSuperSignature' package