NEWS

---

MPAC 1.3.1

• updated citation to point to the journal Bioinformatics

MPAC 1.1.6

• updated pseudocode in vignettes
• added new functions
  • pltConMtf(): to plot consensus pathway submodules
  • pltMtfPrtIPL(): to plot a heatmap of IPLs on proteins from consensus pathway submodules
  • pltSttKM(): to plot Kaplan-Meier curve for patient samples stratified by given protein(s)' pathway states

MPAC 1.1.5

• use 'Multi-omic Pathway Analysis of Cells' for MPAC

MPAC 1.1.4

• updated text in DESCRIPTION

MPAC 1.1.3

• Vignettes
  • added examples on pltOvrHm()
  • added pseudocode for MPAC
  • changed MPAC's full name

MPAC 1.1.2

• pltOvrHm(): use lowercase 'p' instead of 'P' in heatmap colorbar legend
• MPAC's full name is changed to 'Multi-omic Pathway Analysis of Cell'

MPAC 1.1.1

• added new functions
  • pltOvrHm(): to plot a heatmap of over-represented gene sets for clustered samples
  • ppRunPrd(): to prepare required files to run PARADIGM
• updated existing functions
  • conMtf(): use decompose() instead of decompose.graph() for igraph 2.0
  • ppPermInp(): increased default permutations from 3 to 100
  • ppRealInp() and ppRnaInp(): added an option rna_n_sd to set standard deviation range to define RNA state
  • pltNeiStt(): fixed bugs and adjusted output figure height
  • colPermIPL() & fltByPerm(): added a threads option to parallelize
  • runPrd() & runPermPrd(): when no sampleids is provided, all the
    samples in input real_se and perml will be used.
  • subNtw(): entities with NA values in all samples in the input fltmat will be ignored.
• updated tests
  • test-conMtf() & test-subNtw(): use as_edgelist() instead of get.edgelist() for igraph 2.0
  • test-conMtf() & test-ovrGMT(): add upgrade_graph() on extdata

MPAC 0.99.10

Added documentation in inst/scripts/ for the source and derivation of inst/extdata/

MPAC 0.99.1

• Used SummarizedExperiment objects for CNA and RNA matrix in functions:

  • ppCnInp()
  • ppRnaInp()
  • ppPermInp()
  • runPrd()
  • runPermPrd()
  • pltNeiStt()

• Added a function to prepare both CNA and RNA input: ppRealInp()

• Removed GitHub PARADIGM URLs from R code

• Removed dependence on the magrittr package

MPAC 0.99.0

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