analyzeCOMBO: This function calculates significant synergy/antagonism...

Description Usage Arguments Value Author(s) Examples

Description

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

Usage

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analyzeCOMBO(filename, sheet = 1, model, inputFormates, platetype = "384",
  keyposition = 2, selectionkey = "65000", platekey = 7051,
  minThersholdForCVCal = 0.15, minThersholdForCV = 0.3, wells,
  yConcentration, xConcentration, xDrug, yDrug, cellLine,
  survivalFunc = function(x, y, z) {     (x - z)/(y - z) }, nBoot = 5000)

Arguments

filename

Name of file containing experimental data. For MS Excel files, working version of Perl must be present in the executable search path.

sheet

Optional, sheet number if excel file is used for input.

model

bliss or loewe.

inputFormates

Any of these three formates "fmca", "macsynergy" and "others" are supported. Example is provided with macsynergy format and test data for this example can be found in installation directory ("extdata") of COMBIA. See files FluoOptima_384_2014-03-28test_M and testDataM in directory "extdata" for format details of "fmca" and "macsynergy". "others" can be any other format.

platetype

Optional default is 384. Only 384 and 96 well plates are supported.

keyposition

Optional default is 2. Usefull for automated barcoded data.

selectionkey

Optional default is 65000.

platekey

Optional barcode.

minThersholdForCVCal

Optional default is 0.15.

minThersholdForCV

Optional default is 0.3.

wells

wells argument should be in triplet form that is 1-Untreated control wells range, 2-empty wells range and 3-case wells range. Thus in example below (see well argument) experiment has four replicates. "l3:l10","m3:m10","b3:k10" is first replicate. Where "l3:l10" is the location of untreated control values in the testData.csv, "m3:m10" is the background/ empty well well values and "b3:k10" are values after treatment.

yConcentration

Y drug Concentrations.

xConcentration

X drug Concentrations.

xDrug

X drug name.

yDrug

Y drug name.

cellLine

Cell/Experiment name.

survivalFunc

Optional default is function (x,y,z) (x-z)/(y-z) i.e (treated - background)/ (untreated - background).

nBoot

Optional Number of time to bootstrap default is 5000

Value

Stores and show graph/data of synergy/antagonism analyses

Author(s)

Muhammad kashif

Examples

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fl <- system.file("extdata", "testData.csv", package="COMBIA")
wellR <- list(c("l3:l10","m3:m10","b3:k10", "l13:l20","m13:m20","b13:k20", 
           "l23:l30","m23:m30","b23:k30", "l33:l40","m33:m40","b33:k40") )
mdl <- "bliss"
xConc <- c(0.00,  0.20,  0.39,  0.78,  1.56,  3.12,  6.25, 12.50, 25.00, 50) 
yConc <- c(128,  64,  32,  16,   8,   4,   2,   0)
xDrug <- "A"
yDrug <- "B"
cellLine <-"Cell"
analyzeCOMBO(filename = c(fl), model = "bliss", inputFormates = "macsynergy", 
                 wells = wellR, yConcentration = yConc, xConcentration = xConc,
                 xDrug = xDrug, yDrug=yDrug, cellLine = cellLine, nBoot=500)

COMBIA documentation built on May 2, 2019, 7:23 a.m.

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