Synergy/Antagonism Analyses of Drug Combinations

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Documentation for package ‘COMBIA’ version 1.0-4

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applyBliss This function performs synergy analysis based on Bliss model and calculates associated BIs and global BI.
applyLoewe This function calculates Loewe synergy/antagonism and associated BIs.
calculateSynergy Function calculates significant synergy/antagonism in experimental data as per Bliss or Loewe model.
combineDataFromMultipleFiles It combines data from multiple files/experiments into a matrix. Multiple experiments can be performed at the same or different concentration ranges. The function can also be used if there is only one file/experiments.
createUniquePertbs Function to calculate possible unique perturbations of replicates.
cVCal The function calculates coefficient of variance (CV).
extractKey Extracts the barcodes from a dataset, each experimental plate has a barcode in a dataset. Barcodes are extracted from the header of the each plate data from position specified by keyposition argument.
extractReplicateValues On basis of input well ranges, the function extracts values of these ranges from data.
extractValuesFromRange Given a well/wells alphanumeric name e.g. "B2", this function translates it to numeric values.
loeweModel This function applies Loewe model.
readFile Read raw experimental data from a file. This function reads the data from specified (excel,log, txt etc) file and store it in a data frame.
readFluostarPlates Read a file containing raw read outs and calculates survival values. This function calculates survival values as (survival value= treated - empty/ untreated control- empty) of the wells specified in the wells argument. Wells argument should be in triplet form, they are, untreated control well range, empty well range and treated well range. The function also handles the double plate experiments in which one plate is read twice and only one of them is selected.
readFMCAValues Read data from Fluorometric microculture cytotoxic assay (FMCA) data format and clean for outliers.
readMacSynergyValues Read data from macSynergyII format and clean for outliers.
readOtherValues Read data from other than MacSynergy and FMCA format and clean for outliers.
removeOutliers This function removes outliers from data. Outliers are removed if data have more than two replicates. Outlier is defined as an observation that has maximum contribution to data CV when CV is higher than a user defined threshold.
selectPlate Select one readout from the twice read data and store selected values. In those cases where an experiment is read twice, only one readout from each pair is selected. The selection is based on presence of minimum number of "selection key" or read with highest mean is picked in case of tie.
synAntPlot This function prints and saves 2D and 3D plots of synergy/antagonism.
synergySignificant Function "synergySignificant" calculates significant synergy/antagonism concentration combinations and saves synergy/antagonism values.