Feature Set Enrichment Analysis for Metabolomics and
Methods and feature set definitions for feature or gene set
enrichment analysis in transcriptional and metabolic profiling data.
Package includes tests for enrichment based on ranked lists of features,
functions for visualisation and multivariate functional analysis.
Version 0.36, 09.03.2018:
- corrected notorious problems with CRAN
- please CRAN have mercy
- I will sacrifice a virtual goat before submitting
- changed parameter "order.by" to "sort.by" in tmodLimmaTest
- added function pcaplot; tmod no longer depends on pca3d due to
notorious problems with installing rgl on students Mac computers
- limma examples now wrapped in if(require(limma))...
Version 0.34, 10.08.2017:
- added filter.rows.auc option
- Added tmodZtest and tmodWZtest
- Modified gene.labels option for evidencePlot
- Use of the plotwidgets package for pvalEffectPlot (rug, boxpie and pie options)
- Apparently, knitr cache got packed in the package itself, blowing up
its size ten fold.
- Added simpleBoxpie - rectangular plots that are thought better to
visualize areas than regular pie charts
- added a few palette functions from my personal repertoire
- Introduced metabolic modules and created a vignette section for a case
study in metabolomic
- changed the return object of tmodPCA()
- added the "extra" parameter to showModule(); showModule() can take a
data frame or a vector now
- added "row.labels.style" parameter to tmodPanelPlot()
- corrected the malfunctioning testthat test. I HATE TESTTHAT. (Also, I
read it as "test t hat" - and wonder about estimates and Student's t)
- msigDB is broken, it no longer has unique identifiers in the global XML
file. I corrected the import function to make sure identifiers are
- pvalEffectPlot was expecting log10(p-values) rather than p-values. This
has been taken care of.
- evidencePlot can now generate GSEA-style curves (with the "style"
- added Cohen's d estimate and t statistic to tmodLimmaTopTable()
- rewrote evidencePlot: it is now much more flexible