Changelog

pathwayPCA 1.1.4

2020-02-26

  • 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

2019-06-06

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

pathwayPCA 0.99.5

2019-04-12

We have been accepted to Bioconductor! See https://github.com/Bioconductor/Contributions/issues/1000

pathwayPCA 0.99.1

2019-02-01

We are submitting to Bioconductor soon, so we are resolving as many of the BiocCheck() ERRORs, WARNINGs, and NOTEs. See https://github.com/gabrielodom/pathwayPCA/issues/64

pathwayPCA 0.98.0

2018-12-13

See the issues within the “Bioconductor Submission” and “Vignette Work” milestones for detailed descriptions of these changes, their discussion, and motivation: https://github.com/gabrielodom/pathwayPCA/issues

  • 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

pathwayPCA 0.0.0.9000

2018-03-20

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