Optional, sheet number if spreadsheet file is used for input.
model
bliss or loewe.
inputFormates
Any of the three c("fmca","macsynergy","others").
platetype
Optional default is 384.
keyposition
Optional default is 2.
selectionkey
Optional default is 65000.
platekey
Optional barcode.
minThersholdForCVCal
Optional default is 0.15.
minThersholdForCV
Optional default is 0.3.
wells
Defines thes experiment layout in the well ranges, these ranges should be in triplet form that is
1-control wells range, 2-empty wells range and 3-case wells range. An experiment
can have multiple replicates thus having multiple triplicates of well ranges.
yConcentration
Y drug concentrations.
xConcentration
X drug concentrations.
xDrug
X drug name.
yDrug
Y drug name.
cellLine
Cell line/experiment name.
survivalFunc
Optional default is function (x,y,z) (x-z)/(y-z)
where x is combination/drug treatment outcome, y is the untreated control and
z is the background noise.
nBoot
Optional Number of time to bootstrap.
Value
Store and print graphs/data of synergy/antagonism analyses.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(COMBIA)
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: oro.nifti
oro.nifti 0.5.2
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/COMBIA/calculateSynergy.Rd_%03d_medium.png", width=480, height=480)
> ### Name: calculateSynergy
> ### Title: Function calculates significant synergy/antagonism in
> ### experimental data as per Bliss or Loewe model.
> ### Aliases: calculateSynergy
>
> ### ** Examples
>
> fl <- system.file("/raw/testData.xls", 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") )
> sh <- 1
> 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"
> calculateSynergy(filename = c(fl), sheet=1, model="bliss", inputFormates="macsynergy",
+ wells=wellR, yConcentration= yConc, xConcentration=xConc,
+ xDrug=xDrug, yDrug=yDrug,cellLine=cellLine, nBoot=1000)
[1] "Ratio between empty and control 215.34756097561"
[1] "CV for control: 1 : 2.30698484671909"
[1] "Ratio between empty and control 216.431571815718"
[1] "CV for control: 2 : 3.97477131010254"
[1] "Ratio between empty and control 212.255570117955"
[1] "CV for control: 3 : 6.4008999376604"
[1] "Ratio between empty and control 191.453473132372"
[1] "CV for control: 4 : 5.87005801002331"
png
2
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
