Description Usage Arguments Details Value
Process data for a single antigen: fit a standard curve, establish bounds, normalize samples, and save a plot showing the fit and the samples.
1 2 3 4 5 6 7 8 9 10 | 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 |
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 |
asym |
if |
trim.flat |
logical value determining how the values of |
interactive |
logical value. If |
monot.prompt |
if |
rm.before |
logical value indicating if potential outliers should be
removed before the model is fitted. Ignored if |
rm.after |
logical value indicating if potential outliers should be
removed after the model is fitted. Ignored if |
maxrm |
maximum number of outliers to remove. |
set.bounds |
if |
overwrite.bounds |
logical value indicating the option to overwrite
automatically set bounds. Ignored if |
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 |
bgstr |
character string indicating background in the file's "Sample" column. Not case sensitive. |
stddil |
a vector of standard dilutions. If |
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 |
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)***
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