BUG FIX
TO BE ADDED
CHANGES
TO BE ADDED
NEW FEATURES
readBND and readBNET reads MaBoSS style boolean network definition files and converts them to CellNOpt network models - credits for Luis Tobalina
BUG FIX
fix gray boxes in plotOptimResultsPan
in plotOptimResultsPan when errors were greater than 99.9% color were white (instead of red)
c simulator bug fix: at time 0, node that are inhibited and measured were reset to 0 but inhibitors are off. Fix is simple: do not reset inhibitors where time is zero
Fixing issue with time 0 not being simulated properly (see https://github.com/cellnopt/CellNOptR/issues/6) This fixes regression bug following fix made in release 1.11.3
node name in the sif file containing the word AND (e.g. ligand) will not result in an AND-node anymore
Fixing issues with matrix subsetting, when the subsetting converts the matrix to a vector
plotOptimResultsPan: in the computation of root-mean-square error(for coloring the background), the NA data is not counted in the number of data points
CHANGES
Bioconductor's version of the package got merged with the Github's version leading to minor changes
readSIF reads only the unique interactions/lines from the SIF file
plotOptimResultsPan and plotCNOlist plots intermediate cue values (0,1) for CNORode add-on
NEW FEATURES
add readErrors and writeErrors functions in CNOlist: read/write measurement error/variance from/to MIDAS files
toSBML() function writes the model to SBMLqual format
makeCNOlist() can import MIDAS with multiple, continuous cue levels
add new function called crossInhibitedData
BUG FIX
typos leading to failure fixed in cutCNOlist
typos leading to failure in CNOlist if variance were provided
CHANGES
Changed warning into errors in readMIDAS and checkSignals functions
NEW FEATURES
self loop can be read from the SIF files
readSBMLQual do not need to add dummy nodes anymore
BUG FIX
readMIDAS: DV, DA and TR can now be in the specy name
prep4sim can read self loop
plotOptimResultsPan: fix special cases with one or no inhibitors/stimuli
fix bug in cutNONC: notMat was not populated
readSIF: can read and gates coded in big caps as well as small ones
writeMIDAS: manages absence of inhibitors
CHANGES
CNOlist: subfield parameter has been removed. Subfield are automatically found from the header
expandAndGates are not limited to 4 inputs anymore
normaliseCNOlist: EC50 is set to 1 by default
NEW FEATURES
readSBMLQual: a function to read prior knowledge network in SBMLqual format. !! This is a prototype. use with care for now.
cutCNOlist function can cut a MIDAS file over time
BUG FIX
readMIDAS: DV, DA and TR can now be in the specy name
makeCNOlist: bug fixed when only one experiment was present
plotModel: figures where in B and W due to issue in Rgraphviz package
gaBinaryT family: (1) fix bug when only one model found within the tolerance. (2) a faster hash table used in the optimisation.
CHANGES
writeSIF: can overwrite existing file with a parameter
remove cutAndPlotResultsT2: use cutAndPlotResultsTN instead or cutAndPlot
plotOptimResultsPan: NA are now rendered in gray and species are rectangle instead of ellipses. The black line connecting measurements is printed. The ylim for the y axis can be set manually to overwrite the default behaviour.
readSIF can now read relation "A 1 B C D E" as excepted in SIF format.
makeCNOlist/CNOlist: variances available in the structure
NEW FEATURES
CNOdata: a function to fetch data from www.cellnopt.org
plotModel
exhaustive function: a simple exhaustive function to perform optimisation for small models
cutCNOlist: cut a cnolist given a list of species
CNOlist: 3 new methods: length, randomize and plot accepts either one or 2 cnolist arguments.
randomizeCNOlist: function to perform different randomization of the data
model2igraph function
compatCNOlist to convert CNOlist back to old style; used by CNORode
BUG FIX
writeMIDAS uses the new CNOlist class as an input. For back compatibility, the input can also be the data frame output by makeCNOlist; this option was buggy, which is now fixed.
BUG FIX
plotModel can handle CNOlist=NULL as it used to be the case
CHANGES
simulatorT1 and TN have additional check for AND gates with any NA inputs.
BUG FIXES
typo in checkSignals in warning message.
fixing bug (typo) in cutAndPlotResultsT1
BUG FIXES
fixed bug in writeDot function when only 1 stimuli present.
cutNONC function recompte reacID on its own so that if compresion and expansion are not performed, reacID are correct
CHANGES AND UI SIMPLIFICATION
major update that changes User Interface to uniformise the code for users and developers (e.g., readSif function is now called readSIF and prep4Sim is prep4sim). Similarly many arguments are not required anymore. For instance, indexList and simList are not required anymore (for back compatibilty these 2 arguments are usually kept and set to NULL).
improvment of plotModel function to have more graphviz options
gaBinary default initBstring argument is set to ones.
MAJOR refactoring to merge T1, T2, TN functions (cutAnPlot, gaBinary, simulator).
simulateTN combines simulateT1 and simulateTN so only one function is required.
gaBinaryT2 is deprecated. Use TN version instead.
gaBinaryT1 and TN do no need the indexList and simList parameters anymore
preprocessing now returns only the model. indices are not required anymore. preprocessing can now handle model without cnolist provided (e.g. for expansion only)
add a cutAndPlot dispatcher that calls the proper cutandPlotResultsTX function.
cutSimList argument called bitString renamed bString (developers)
computeScoreT1, cutSimList had an argument called bitString. it is now called bString and this convention is used throughout the code (e.g., bStringT1 not bitStringT1) simlist and indexlist are now optional are after the bString argument.
show argument removed from cutAndPlot function family
NEW FEATURES
c Simulator implemented making the optimisation much faster.
steady states extended from T1 and T2 to any time TN
add a CNOlist class that is now used throughout the code (has a plot method that replaces plotCNOlist calls)
add plotParams parameter in cutAndPlot family.
hash table in gaBinaryT1 (maxSizeHashTable as optional argument)
add cutModel function to make code more modular (for developers)
add mapBack function
add computeScore functions to make the code modular.
conversion functions sif2graph, model2sif, graph2sif added to the package
add writeMIDAS function
add writeSIF function
add prior knowledge bitstring in the GA algorithm (T1 and T2)
add a test suite in tests directory