1.10.0

Improvements to graphical interface functions:

• New launchDrugSetEnrichmentAnalysis() function to analyse drug set enrichment and visualize respective results
• launchCMapDataLoader():
  • Now allows to load multiple CMap perturbation types simultaneously
  • Keep selected timepoint, dosage and cell line options when selecting another perturbation type
  • Add bubble plot of CMap perturbation types
• launchResultPlotter():
  • Now allows to view tables below specific plots and drag-and-select those plots to filter data in those same tables
  • When plotting targeting drugs and similar perturbations, update available columns and correctly use user selected column to plot
• launchMetadataViewer() now correctly parses values from Input attributes as numeric

Major changes

• prepareCMapPerturbations(): directly set perturbation type, cell line, timepoint and dosage conditions as arguments
• rankSimilarPerturbations() and predictTargetingDrugs():
  • Avoid redundant loading of data chunks, slightly decreasing run time
  • Lower memory footprint when using NCI60's gene expression and drug sensitivity association (now available in HDF5 files) by loading and processing data in chunks
  • Faster GSEA-based score calculation (up to 4-7 times faster)
  • New threads argument allows to set number of parallel threads (not supported on Windows)
  • New chunkGiB argument allows to set size of data chunks when reading from supported HDF5 files (decreases peak RAM usage)
  • New verbose argument allows to increase details printed in the console
• prepareDrugSets(): allow greater control on the creation of bins based on numeric columns, including the setting of maximum number of bins per column and minimum bin size
• analyseDrugSetEnrichment() and plotDrugSetEnrichment(): allow to select columns to use when comparing compound identifiers between datasets

Bug fixes and minor changes

• filterCMapMetadata(): allow filtering CMap metadata based on multiple perturbation types
• prepareDrugSets(): fix issues with 3D descriptors containing missing values
• plot():
  • Fix wrong labels when plotting targetingDrugs objects
  • Avoid printing "NA" in labels identifying metadata for perturbations
• plotTargetingDrugsVSsimilarPerturbations():
  • Fix highlighting of plot points depending whether drug activity is directly proportional to drug sensitivity
  • Include rug plot
• When subsetting a perturbationChanges or an expressionDrugSensitivityAssociation object, passing only one argument extracts its columns as in previous versions of cTRAP (similarly to when subsetting a data.frame)
• analyseDrugSetEnrichment(): for the resulting table, the name of the first column was renamed from pathway to descriptor