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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 |