pathwayPCA 1.1.4


  • Exported the aespca() function for use in the rnaEditr:: package (currently in development)
  • Reduced R’s version requirement to 3.1 for legacy user compatibility
  • Cleaned up formatting of examples
  • Updated website
  • Cleaned up examples in vignette 5
  • Reformatted NEWS file to put newest news first (dumb mistake on Gabriel’s part)

pathwayPCA 1.1.1


Our build on Bioconductor 3.9 devel fails for the second vignette. This patch resolves this issue.

pathwayPCA 0.99.5


We have been accepted to Bioconductor! See

pathwayPCA 0.99.1


We are submitting to Bioconductor soon, so we are resolving as many of the BiocCheck() ERRORs, WARNINGs, and NOTEs. See

pathwayPCA 0.98.0


See the issues within the “Bioconductor Submission” and “Vignette Work” milestones for detailed descriptions of these changes, their discussion, and motivation:

  • Standardized naming conventions to UpperCamelCase for consistency
  • Changed class name pathwaySet -> pathwayCollection
  • Added functions SubsetPathwayData, getPathPCLs, LoadOntoPCs, write_gmt, getSampleIDs, CheckSampleIDs, getTrimPathwayCollection, getPathwayCollection, CheckPwyColl, CheckAssay, and print and subset methods for pathwayCollection objects
  • Added sample ID requirements for input assays and phenotype data. Changed the phenotype required class from anything to a data frame.
  • Made the lars implementation a touch more robust. If the algorithm fails to converge, then we default back to regular SVD
  • The AESPCA function can also return pathway-specific vanilla PCA. Also, we inspected the parametric p-values compared to the permutation-based p-values. They congruence is nearly perfect for all of the data sets we tested. Thus, we changed the default p-value estimation method for AESPCA to be parametric.
  • Method functions (*_pVals()) now return a list with the p-values data frame, list of PC vectors (in a data frame), and list of loading vectors (in a data frame). The getPathPCLs function will subset this list to return the PCs, loadings, and administrivia of the method PCA output for a single pathway
  • added the June homo sapiens pathway collection from WikiPathways: wikipwsHS_Entrez_pathwayCollection
  • Lily wrote a vignette geared to show off the diverse functionality of the package, so this is the new main vignette. I broke off the plots from chapter 4 into their own chapter. The five vignettes I wrote are now supplemental chapters
  • updated vignettes and website



  • Added a file to track changes to the package.
  • Built website.