diskImageR: calcMIC – R documentation

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calcMIC

Convert RAD to MIC based on built-in or provided parameters or datasets

Description

Used to convert RAD into MIC. In all cases the linear relationship is log2(MIC) regressed onto RAD^2. This conversion can be based on a) existing built-in data from a number of species/drug combinations, b) a user-supplied slope and intercept of log2(MIC) regressed on RAD^2 for the species/drug combination of interest, c) a user supplied file containing MIC information from lines previously analyzed by diskImageR for RAD, or d) a user supplied file containing both RAD and MIC information. Note that user-supplied data should be MIC and RAD, not log2(MIC) and RAD^2 (the function will do this authomatically).

Usage

calcMIC(projectName, type = "df", RAD = "20", height = 4, width = 6,
  addBreakpoints = TRUE, savePDF = TRUE, popUp = TRUE)

Arguments

`projectName`	the short name you have been using for the project.
`type`	specify whether the dataset to use is a dataframe with all data ("df") or an aggregated dataframe ("ag")
`RAD`	a numeric value the the critical level of the radius of inhibition (i.e., resistance) parameter to use for MIC. Currently only `RAD` = "80" (80% reduction in growth), `RAD` = "50" (50% reduction in growth), and `RAD` = "20" (20% reduction in growth) are supported [Default = "20"]
`height`	a numeric value indicating the height of the pdf file generated
`width`	a numeric value indicating the width of the pdf file generated
`addBreakpoints`	Indicates whether to add breakpoint lines to the standard curve plot (if the user has supplied data to generate a standard curve)
`savePDF`	a logical value indicating whether to save a PDF file or open a new quartz window. Defaults to TRUE (saves a pdf file).
`popUp`	a logical value indicating whether to pop up the figure after it has been created

Value

In all cases the function will return an updated .csv file that contains the MIC values that correspond to calculated RAD values in the directory "parameter_files" in the main project directory. If the user has supplied their own MIC data the function will also save the calculated model parameters into a separate file and will plot the linear relationship and line of best fit.

diskImageR

A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays

v1.0.0

GPL-3

Authors

Aleeza Gerstein [aut, cre], Inbal Hecht [ctb]

Initial release