cellGrowth (version 1.16.0)

bandwidthCV: Bandwidth cross-validation

Description

Perform cross-validation to detect optimal bandwidth

Usage

bandwidthCV(well, fileParser = readYeastGrower, getWellIds = getWellIdsTecan, bandwidths = seq(0.5 * 3600, 10 * 3600, length.out = 30), nFold = 10, nWell = 100, cutoff = 0.95, calibration = identity, scaleY = log2)

Arguments

well

well dataframe. See wellDataFrame.

fileParser

Converts the file generated by the machine to proper R format. See readYeastGrower for 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.

bandwidths

vector of bandwidths to test on

nFold

integer. In how many parts is the sample divided for cross-validation?

nWell

integer. How many wells out of the well dataframe will be used for cross validation?

cutoff

scalar between 0 and 1. See details.

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

scaleY

function applied to the calibrated data.

Value

list with entries

bandwidth

"optimal" bandwidth

well

well dataframe

bandwidths

tested bandwidths

err2

squared error

err2std

Standard deviation of squared error

muStd

Standard deviation of max growth rate

oneStdOfMini

bandwidths within one std of best

Details

This function needs a few minutes time. The "optimal" bandwidth is the largest bandwidth which is in 95% (cutoff parameter) of all cases within one standard deviation of the best bandwidth. This should make the derivative of the fitted curve more robust. 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.

Examples

folder <- system.file("extdata", package="cellGrowth")
well <- wellDataFrame(file.path(folder, "plateLayout.txt"), file.path(folder,"machineRun.txt"))

## for a fast example, we use nWell = 1 here. Use a large number (default 100) for real life applications
bw <- bandwidthCV(well, nWell=1)