qfa.normalize: Function to normalize QFA data
In JulBaer/baQFA: Quantitative Fitness Analysis Version 2

qfa.normalize

R Documentation

Function to normalize QFA data

Description

This function normalizes the input data to be in the range of o to 1. (Input data.frame preferentially generated by colonyzer.read or GC2QFA). The target values need to be stored in a column named Growth. Different methods for normalization are provided. "All", the default methods, normalizes all data within the data.frame. The method "Plate" normalizes per plate indicated by a distinct "Barcode" within the data.frame. Method "Sample" normalizes over each position indicated by Row and COlumn and distinct Barcode. Method "ZeroShift" subtracts from each position its own minimal value to move the starting values of the growth curve to zero. Method "Adjust" is useful if at one timepoint an arbitrarily high value was recorded. This can happen if the light was considerably higher at one timepoint due to experimental error. If this only happens infrequently, the user can specify the AdjInd as the position of measurement to be replaced with the value of AdjTo. Usually AdjTo should be AdjInd+/-1. Use cautiosly. The last method "Reference" normalizes the given data but does not take the min and max values of itself but the values MaxVal and MinVal provided by the user. This may be useful if comparing datasets generated with slightly varying imaging settings.

Usage

qfa.normalize(
  dta,
  NormMode = "All",
  AdjTo = NA,
  AdjInd = NA,
  MaxVal = NA,
  MinVal = NA
)

Arguments

`NormMode`	String. This indicates the method used for the normalisation. For explanations, see the text above. Possible options: All, Plate, Sample, ZeroShift, Adjust, Reference.
`AdjTo`	Numerical. Only necesarry to specify for the Adjust method. Indicates the index to take the value from to replace at index AdjInd.
`AdjInd`	Numerical. Only necessary to specify for the Adjust method. Indicates the index of the growth value to be replaced with the value at index AdjTo.
`MaxVal`	Numerical. Only necessary to specify for the Reference method. This indicates the potential max value that could have been recorded.
`MinVal`	Numerical. Only necessary to specify for the Reference method. This indicates the potential min value that could have been recorded.
`path`	dta data.frame. This should contain data generated by either GC2QFA or colonyzer.read and a column named Growth in which the growth data is stored. This column's data will be normalized.