OGA: OGA (Outgrowth Analysis)

In labmccormick/SPOCK: Analysis yeast density over time to determine growth and survival data

Description

OGA calculates doubling times. The process is to subtract blank wells, then smooth high frequency noise using a Butterworth filter. OGA then identifies an interval of exponential growth. This is done by picking an end time for exponential growth by defining the inflection point of exponential growth as determined by the 1st derivative (diff) ul, and a beginning time for exponential growth by a heuristically defined minimum slope change. The doubling time is then calculated between these begining and end points.

Usage

OGA(
  autoinput = TRUE,
  nestdataframe = dfs,
  homedir = getwd(),
  ladder = TRUE,
  laddername = "ladder.csv",
  repladder = 3,
  blank = TRUE,
  blankname = "BLANK",
  create.plot = TRUE,
  stringencyfilt = 3,
  frequencyfilt = 0.05,
  measureInterval = 15,
  lowerlimitslope = 0.01,
  maxinflectionpoint = 1.3,
  LimitNoGrowth = 0.9,
  statsDT = TRUE,
  bacteria = 45,
  laglimit = 0.1,
  rmflagged = TRUE
)

Arguments

autoinput	BOOL parameter, if TRUE then automatically read in all .csv files in current working directory for outgrowth analysis. These csv files are autoinput into data frames, otherwise OGA expects to find a value for data frames.
nestdataframe	if autoinput is FALSE, then instead you need to pass a nested dataframe to analyze to this parameter.
homedir	Home Directory= working directory containing RAW .csv files from plate reader, in Example.csv format.
ladder	BOOL parameter, if TRUE then OGA creates calibration ladder from laddername and calibrates RAW data.
laddername	Name of ladder.csv file (in the same directory as RAW .csv files).
repladder	Number of technical replicates in ladder (see example).
blank	Do you have blanks (wells with no inoculum and only media) in the csv files (TRUE/FALSE)
blankname	Name used for blank wells, this name is case sensitive and must match exactly with the csv files.
create.plot	BOOL parameter, if TRUE then OGA passes RAW files to create.plots to produce plots? (TRUE/FALSE).
stringencyfilt	What order to use for stringency of Butterworth Filter.
frequencyfilt	What cutoff to use for frequency of Butterworth Filter.
measureInterval	Time between OD measurements in minutes.
lowerlimitslope	Slope above which growth is considered exponential.
maxinflectionpoint	OD above which the exponential growth phase cannot occur.
LimitNoGrowth	What is the OD limit to signal no growth detected/insufficient information for complete growth curve.
statsDT	BOOL parameter, if TRUE, OGA passes results files to statsDT(TRUE/FALSE)
bacteria	Limit below which doubling-time is marked as bacterial contamination, for yeast. If measuring bacterial growth, set = 0.5.
laglimit	OD above which marks the end of the lag-phase.
rmflagged	This determines if flagged wells are removed from statistics. default=TRUE

labmccormick/SPOCK documentation built on May 25, 2021, 5:25 p.m.