GC2QFA: Converting plate reader growth curve output for QFA usage

In JulBaer/baQFA: Quantitative Fitness Analysis Version 2

Converting plate reader growth curve output for QFA usage

Description

This function transforms the output of plate reader growth curves saved in 'Time' format to a data.frame suitable for calls to qfa.fit2. Together with the growth curve data (GC) as a data.frame, a second data.frame containing metadata information (info) about the wells of the GC data.frame. There are specific formatting conditions that need to be met by the input data.frames. There needs to be a column named 'Time' or 'time' indicating time for the GC data.frame. This column should either be in hours, min or days and this information is specified with 'timeFormat'. The other column names of the GC data.frame should indicate the 'Well' name. Each of these wells need to be represented with one row in the info data.frame. The info data.frame needs to have a calumn called 'Well' with these matching well names. The second mandatory column should be named 'Condition' and describes the content of each well. Here, the user can also specify which wells are blanks to be used as a correction mean. Additionally, the user needs to specify the numbers of rows and cols. The default values are for 96 well formats. The output data.frame contains aggregated data with one row per well and time combination together with all info data.frame data and is ready to be used with qfa.fit2. The output data is stored in columns named 'OD_raw' and 'OD_calib'.

Usage

GC2QFA(
  GC,
  info,
  rows = 8,
  cols = 12,
  correction = "blank",
  timeFormat = "min",
  ExpName = "Default",
  Inoc.Time = "2019-01-20 03:21:00",
  Library.Name = "Default",
  MasterPlate.Number = 1,
  ScreenID = "SaureusTest",
  Screen.Name = "SauresTest",
  Treatments = 1,
  shiftZero = F
)

Arguments

GC	data.frame. This contains the growth curve data from a plate reader stored in 'Time' format. Column names should represent well names. One column needs to be named 'Time' and indicate the timecourse of the growth curve either in minutes, hours or days. No other columns should be present
info	data.frame. This contains the metadata of the GC data.frame. Two columns are necessary: One named 'Well' corresponding to the column names of the GC data.frame and a second named 'Condition' describing the well contents. All other columns are added to the final output of GC2QFA
rows	numerical. Indicating number of rows of the growth curve plate. Default set to 8 for 96 well formats
cols	numerical. Indicating number of cols of the growth curve plate. Default set to 12 for 96 well formats. Please note that the length of the info data.frame needs to match rows times cols and that the number of columns of the GC data.frame needs to match rows times cols + 1 (for the time column)
correction	String. Indicating the type of correction method used. Either 'blank', 'individual' or 'none'
timeFormat	String. Indicating the format of the 'Time' column of the GC data.frame. Either 'min', 'h' or 'd'
ExpName	String. Necesarry information for qfa.fit2 to describe the experiment (Barcode). Use this as identifier for each plate/run to ensure smooth operation of qfa.fit2 and following functions
Inoc.Time	String. Inoculation time start in specific format 'YYYY-MM-DD hh:mm:ss'. Necesarry for qfa.fit2 to calculate timecourse
Library.Name	String. Necesarry information for qfa.fit2 to describe the experiment
MasterPlate.Number	Numerical. Necesarry information for qfa.fit2 to describe the experiment
ScreenID	String. Necesarry information for qfa.fit2 to describe the experiment
Screen.Name	String. Necesarry information for qfa.fit2 to describe the experiment
Treatments	Numerical or String. Necesarry information for qfa.fit2 to describe the experiment
shiftZero	logical. Indicating if each wells growth curve should be normalised to start from 0 by subtracting from each well its minimum

Details

Different calibration methods can be used. The default method is 'blank'. A mean of all wells indicated as 'blank' within the info data.frame column 'Condition' for each measurement timepoint is calculated. This mean is then subtracted from all other wells. Another options is 'individual': the min value of each well is subtracted from itself. With 'none', no calibration is calculated.

JulBaer/baQFA documentation built on Feb. 19, 2023, 10:32 p.m.