Synergy/Antagonism Analyses of Drug Combinations


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Documentation for package ‘COMBIA’ version 1.0.6

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analyzeCOMBO This function calculates significant synergy/antagonism according to Bliss or Loewe model and creates scientific publication ready graphs.
applyBliss Function calculates Bliss Synergy, associated BIs and global BIs
applyLoewe This function calculates Loewe synergy/antagonism and associated BIs
calculateSi Calculates survival indices (S.Is) for a range of wells (casewells). S.Is for a range of wells are calculated, that range is specified at the third place of wells argument list. This function call the rangemean function to calculate the mean of the range of the specified range. S.I is calculated by (Case well- meanofemptyrange/mean of controlwell- meanofemptyrange). In the wells argument one should provide arguments in the triplet form that is first one is control data range, second one is the empty data range while third one is the control range.
combineDataFromMultipleFiles Combine data from multiple files
createUniquePertbs Function to make unique perturbations of the replicates these will be used incase if CV is greater than threshold.
cVCal This function calculates CV
extractKey Extracts the keyvalues (Barcode) from a dataset, every plate needs barcode. Keyvalues are extracted from the header of the plates at the position specified by keyposition argument.
extractReplicateValues This function will takes a list of ranges removes case wells and extract replicate values separately
extractValuesFromRange This function extract numerical indices of a given range e-g B2
loeweModel This function applies Loewe Model
readFile Reads 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 and process it to calculate the Survival indeces(S.I). This function calls other functions to complete its task. It reads a file to separate and regenerate the missing platekeys. Checks are performed to keep regenerated missing keyvalues in sync with data. It calculates survival indeces of the provided control wells, where wells should always be in triplet form that is control well range, empty well range and case well range. It can also handle the double plate experiments in which one plate is read twice and only one of them is selected in S.I calculations. Secondly it can also read the data from the file where a plate is read only one time, still it cope with variations if an experiment is repeated twice or many time in adjacent rows in the file.
readFMCAValues Read data from raw FMCA format and clean for outliers
readMacSynergyValues Read data from macsynergyII formate and clean for outliers
readOtherValues Read data from raw format and clean for outliers
removeOutliers This function Remove Outliers
selectPlate Select one of the two read plates and built a hashtable. One plate from each pair of the read plate is selected in case of double plate experinment on the basis of presence of minimum selection key and if none have maxed out values then one with highest mean value is picked.
synAntPlot This function plots the synergy analysis 2D and 3D graphs
synergySignificant Function calculates significant synergy/antagonism