data.frame with mandatory columns directory,
filename, well. See wellDataFrame
plot.folder
see details
model
model to choose for fitting growth curve
fileParser
Converts the file generated by the
machine to proper R format. See
readYeastGrower for details.
xlab
plot parameter
ylab
plot parameter
scaleX
useful if you want to get the doubling in
another unit, e.g. days instead of seconds.
scaleY
function applied to the calibrated
data.
calibration
function or list of
functions. If function, calibration is applied to
all raw data. If list, the well dataframe must contain a
column machine. Depending on that column the
according function in the list is applied to the raw
data. See details
getWellIds
function or vector. If function its
parameter is the return value of fileParser. It should
return a vector containing the well ids (e.g. A01, A02,
...). You can set the well ids vector directly. See
getWellIdsTecan.
locfit.h
bandwidth parameter for local polynomial
fitting. If set to "bandwidthCV" bandwidth is
automatically selected through bandwidthCV
bandwidths
passed to bandwidthCV if
locfit.h="bandwidthCV"
nFold
passed to bandwidthCV if
locfit.h="bandwidthCV"
nWell
passed to bandwidthCV if
locfit.h="bandwidthCV"
cutoff
passed to bandwidthCV if
locfit.h="bandwidthCV"
...
Parameter is passed to
fitCellGrowth
Details
Essentially a wrapper for fitCellGrowth.
The function gets a well object and fits a growth curve
on all wells. It computes the doubling frequency observed
in a well and extracts the maximal growth rate (
1/minimal doubling time). The raw values from the machine
might not be directly optical densities (OD), which is
needed to infer doubling time. Calibration functions for
each machine can be provided to map raw values into OD
using the calibration parameter. If the parameter
plot.folder is set, the function creates a folder within
plot.folder for each file in the well object. For each
well a plot is written into that folder, named
well_id.png.
Value
dataframe with entries
maxGrowthRate
maximal
growth rate
pointOfMaxGrowthRate
datapoint where
growth rate is maximal
max
inferred maximum among
the time points
pointOfMax
datapoint of the max
fitted value
Author(s)
Julien Gagneur and Andreas Neudecker
See Also
fitCellGrowth
Examples
plateLayout <- system.file("extdata", "plateLayout.txt", package="cellGrowth")
machineRun <- system.file("extdata", "machineRun.txt", package="cellGrowth")
well <- wellDataFrame(plateLayout,machineRun)
cal <- function(x){x+1}
fit <- fitCellGrowths(well,plot.folder="data",calibration=cal)
Results
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(cellGrowth)
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/cellGrowth/fitCellGrowths.Rd_%03d_medium.png", width=480, height=480)
> ### Name: fitCellGrowths
> ### Title: Fit multiple growth curves
> ### Aliases: fitCellGrowths
>
> ### ** Examples
>
> plateLayout <- system.file("extdata", "plateLayout.txt", package="cellGrowth")
> machineRun <- system.file("extdata", "machineRun.txt", package="cellGrowth")
> well <- wellDataFrame(plateLayout,machineRun)
> cal <- function(x){x+1}
> fit <- fitCellGrowths(well,plot.folder="data",calibration=cal)
treating 4 unique tecan files.
treating file /home/ddbj/local/lib64/R/library/cellGrowth/extdata/./Plate1_YPMalt.txt
treating file /home/ddbj/local/lib64/R/library/cellGrowth/extdata/./Plate1_YPFruc.txt
treating file /home/ddbj/local/lib64/R/library/cellGrowth/extdata/./Plate2_YPMalt.txt
treating file /home/ddbj/local/lib64/R/library/cellGrowth/extdata/./Plate2_YPFruc.txt
Warning messages:
1: In fitCellGrowth(x = x[ii], z = z[ii], model = model, locfit.h = locfit.h, :
Maximal population reached close to the border. You can identify the well by testing for pointOfMax
2: In fitCellGrowth(x = x[ii], z = z[ii], model = model, locfit.h = locfit.h, :
Maximal population reached close to the border. You can identify the well by testing for pointOfMax
3: In fitCellGrowth(x = x[ii], z = z[ii], model = model, locfit.h = locfit.h, :
Maximal population reached close to the border. You can identify the well by testing for pointOfMax
>
>
>
>
>
> dev.off()
null device
1
>