Changes in version 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 Changes in version 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 Changes in version 0.0.0.9000 2018-03-20 - Added a NEWS.md file to track changes to the package. - Built website.