Major changes

  • Switched away from R’s standard reference classes to R6 classes (#57).
  • httr is now the new dependency replacing RCurl (#54).

ImmuneSpaceConnection class

  • The connection class is now based on the R6 class system (#57).
  • getGEMatrix method can now access the raw matrix for a cohort using the ‘outputType = raw’ argument and return probe-level (microarray) or gene-counts (RNAseq), non-normalized or summarized data (#63).
  • getGEmatrix method now has a boolean ‘verbose’ argument that when set to TRUE will print information on how the matrix was constructed, such as normalization procedure and annotation version (#66).
  • Updated print method to show a prettier summary of the object (#62).
  • getDataset method will now return an empty data frame for invalid dataset names (#68).
  • Restructured fields and methods into public and private (#59, #60).
  • Some fields and methods were renamed to be consistent with the existing naming convention (verb + camelCase), and others are documented for users (#59, #60).
  • These are currently available fields and methods. Please note the name changes and deprecated fields and methods in the new version. Check the class documentation for detailed description of fields and methods.
  • study
  • availableDatasets (renamed from available_datasets)
  • cache (renamed from data_cache)
  • config
  • print (renamed from show)
  • listDatasets
  • listGEMatrices (renamed from GeneExpressionMatrices)
  • listGEAnalysis
  • listParticipantGroups
  • getDataset
  • getGEMatrix
  • getGEAnalysis
  • getGEFiles
  • getGEInputs (renamed from GeneExpressionInputs)
  • getParticipantData
  • addTreatment
  • mapSampleNames (renamed from EMNames)
  • plot (renamed from quick_plot)
  • clearCache (renamed from clear_cache)

Minor bug fixes and improvements

  • Reorganized the file structure in /R (#60).
  • Fixed .onLoad() note on R CMD CHECK (#61).
  • Removed setting of RCurlOptions cainfo and CA certificates as it is no longer needed for httr (#61).
  • Modified user agent to capture more information about user’s R environment (i.e., “R/3.4.3 (Linux x86_64) Rlabkey/2.2.0 ImmuneSpaceR/1.7.2”) (#61).
  • Built a pkgdown site (#67).
  • Added an argument (mc.cores) to checkRawFiles method as a temporary fix for httr’s bug (not working well with mclapply) (#64).
  • Updated checkStudyCompliance (#65).