processLum: Process raw Luminex files
In Greenhouse-Lab/lumfit: Luminex Data Processing

Description Usage Arguments Details Value

View source: R/processLum.R

Process data for a single antigen: fit a standard curve, establish bounds, normalize samples, and save a plot showing the fit and the samples.

processLum(antigen, fname, fdir = NULL, plotdir = NULL,
  xvar = "logConc", yvar = "logMFI", model = "sigmoid",
  Alow = NULL, asym = TRUE, trim.flat = TRUE, interactive = TRUE,
  monot.prompt = FALSE, rm.before = FALSE, rm.after = interactive,
  maxrm = 2, set.bounds = interactive, overwrite.bounds = FALSE,
  ifix = NULL, dtype = "Median", stdstr = "std|stand",
  bgstr = "blank|background", stddil = NULL, smpdil = 1000,
  optmethod = "Nelder-Mead", maxit = 5000, nwells = NULL, nsep = 2,
  ncolmax = 105, dformat = "%m/%d/%Y", width = 6, height = 6,
  ptcol = "firebrick3", rugcols = c("cadetblue", "purple", "red"), ...)

`antigen`	character string.
`fname`	name of the file that contains raw data.
`fdir`	directory where the file is located (alternatively, full path can be included in `fname`).
`plotdir`	directory for the plots to be saved.
`xvar, yvar`	character strings for the variables used to fit a standard curve.
`model`	the model to be fit.
`Alow`	lower asymptote for the sigmoid model. If `NULL`, the lower asymptote will be estimated, adding an extra parameter to the model. To fix the asymptote at the level of background, specify `"bg"`. Numeric value of `Alow` will force the asymptote to be fixed at the provided level.
`asym`	if `TRUE`, asymmetry in the fit is allowed, adding an extra parameter to the model.
`trim.flat`	logical value determining how the values of `yvar` are trimmed. If `TRUE`, they will be trimmed at the bounds where the curve starts to flatten out (automatically determined as maxima of the third derivative of the function). If `FALSE`, `yvar` will be trimmed at extrema, defined as the range of standards or asymptotes of the fit (whichever are less extreme).
`interactive`	logical value. If `TRUE`, the user is prompted to evaluate the standards (and/or the fit) and asked to remove outliers if needed. `TRUE` value takes precedence over `rm.before` and `rm.after`: if both are `FALSE`, `rm.after` is reset to `TRUE`.
`monot.prompt`	if `TRUE`, the user is prompted to evaluate the standards and possibly remove outliers if the standards are not monotonic (increasing). `FALSE` value is ignored if `interactive` is `TRUE`.
`rm.before`	logical value indicating if potential outliers should be removed before the model is fitted. Ignored if `interactive` is `FALSE`.
`rm.after`	logical value indicating if potential outliers should be removed after the model is fitted. Ignored if `interactive` is `FALSE`.
`maxrm`	maximum number of outliers to remove.
`set.bounds`	if `TRUE`, the user is given the option to manually set the bound that is not set automatically. In that case, the prompt appears even if `interactive` is `FALSE`.
`overwrite.bounds`	logical value indicating the option to overwrite automatically set bounds. Ignored if `interactive` is `FALSE`.
`ifix`	sorted integer vector of length 3 with indices of standards to be used for getting starting values for optimization.
`dtype`	character string for data type in the file.
`stdstr`	character string indicating standards in the file's "Sample" column. Not case sensitive. If `""` (empty string), standards will be determined by the pattern "1/" only.
`bgstr`	character string indicating background in the file's "Sample" column. Not case sensitive.
`stddil`	a vector of standard dilutions. If `NULL`, dilutions are inferred from the file's "Sample" column. Non-null value can be used to exclude some dilutions from model fitting.
`smpdil`	dilution used for the samples.
`optmethod`	method to be used in optimization.
`maxit`	maximum number of iterations in optimization.
`nwells`	number of wells. If `NULL`, inferred from the file.
`nsep`	number of lines separating different data types in the file.
`ncolmax`	maximum number of columns in the file.
`dformat`	date format in the file.
`width, height`	optional parameters for the final saved plot.
`ptcol`	color of the standard points on the plot.
`rugcols`	vector of three colors for the rugplot, which indicates sample values (inside the bounds, between the bounds and extrema, and beyond extrema).
`...`	further graphical parameters.

details to be added

A list of length two. The first element is a data frame that contains the results; the second is a character string with a flag containing information about removed points, failure to fit the model, manually set bounds, and/or an optional custom note provided by the user during an interactive model-fitting procedure. ***optional return of the number of trimmed samples (then a list of length three)***

Greenhouse-Lab/lumfit documentation built on July 20, 2020, 8 p.m.