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COMBIA (version 1.0.6)

Synergy/Antagonism Analyses of Drug Combinations

Description

A comprehensive synergy/antagonism analyses of drug combinations with quality graphics and data. The analyses can be performed by Bliss independence and Loewe additivity models. 'COMBIA' provides improved statistical analysis and makes only very weak assumption of data variability while calculating bootstrap intervals (BIs). It is based on heteroscedasticity controlled resampling (bootstrapping) and includes a global (omnibus) test. Finally, package shows analyzed data, 2D and 3D plots ready to use in research publications. 'COMBIA' does not require manual data entry. Data can be directly input from wet lab experimental platforms for example fluostar, automated robots etc. One only needs to call a single function, analyzeCOMBO(), to perform all analysis (examples are provided with sample data).

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Version

Install

install.packages('COMBIA')

Monthly Downloads

32

Version

1.0.6

License

GPL (>= 2)

Maintainer

Muhammad Kashif

Last Published

October 8th, 2018

Functions in COMBIA (1.0.6)

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.

extractValuesFromRange

This function extract numerical indices of a given range e-g B2

This function applies Loewe Model

Read data from raw FMCA format and clean for outliers

synergySignificant

Function calculates significant synergy/antagonism

This function plots the synergy analysis 2D and 3D graphs

readOtherValues

Read data from raw format and clean for outliers

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.

readMacSynergyValues

Read data from macsynergyII formate and clean for outliers

This function Remove Outliers

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.

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

Function calculates Bliss Synergy, associated BIs and global BIs

This function calculates CV

createUniquePertbs

Function to make unique perturbations of the replicates these will be used incase if CV is greater than threshold.

This function calculates significant synergy/antagonism according to Bliss or Loewe model and creates scientific publication ready graphs.

This function calculates Loewe synergy/antagonism and associated BIs

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