stdCurve: Fit data to a standard curve

In shirewoman2/LaurasHelpers: Miscellaneous Helper Functions for Common PK or Analytical Chemistry Tasks

Fit data to a standard curve

Description

stdCurve, which was designed with mass spectrometry data in mind, fits concentration and signal data to a standard curve and returns the calculated betas, a plot of the standard curve, the data that were used to generate the fitted line, and the original data that were used to generate the standard curve.

Usage

stdCurve(
  DF,
  rawPeak,
  rawIS,
  normPeak,
  nominal,
  poly = "1st",
  weights = NULL,
  omit = NA,
  IDcol = NA,
  colorBy,
  useNLS_outnames = TRUE
)

Arguments

DF	The input data.frame with columns containing the nominal analyte concentration and the instrument response
rawPeak	The unadjusted instrument response column. Ignore this if data are already normalized by internal standard.
rawIS	The internal standard column name. This is ignored if normPeak is provided.
normPeak	The column containing instrument response normalized by internal standard. Use this if the data are peak heights or areas already divided by the IS peak height or area.
nominal	The column with the nominal concentrations or masses.
poly	Should the data be fit to a 1st or 2nd order polynomial? Options: "1st" or "2nd".
weights	Weighting scheme to use for the regression. User may supply a numeric vector of weights to use or choose from "1/x", "1/x^2", "1/y" or "1/y^2". If left as NULL, no weighting scheme will be used. Be careful that you don't have any infinite values or this will fail!
omit	An index of which, if any, samples to omit from the curve. These samples will be depicted as red open circles in the graph but will not be included in the regression. The red color for omitted points overrides any other choices for colorBy.
IDcol	Optional column with sample IDs
colorBy	What column to color the points by in the standard curve graph. If not set, all points will be black.
useNLS_outnames	TRUE or FALSE for whether the object "Fit" should be the standard, list output from nls or nls2. If set to FALSE, the output will be a data.frame of the coefficients with column names "Beta", "Estimate", "SE", "tvalue" and "pvalue".

Value

Output is a list of the following named objects:

Fit

The fitted parameters

CurvePlot

A plot of the data and the fitted line

CurveDF

A data.frame of the points used for graphing the fitted line.

Data

The original data with a column of the calculated concentration or mass as a percent of the nominal.

Examples

data(ExStdCurve)

# Using a peak ratio that's already been calculated
stdCurve(ExStdCurve,
         normPeak = MET.peakarearatio,
         nominal = MET.nominalmass,
         poly = "2nd")

# Having 'stdCurve' calculate the peak ratio and making the fitted
# coefficients a data.frame rather than a list
stdCurve(ExStdCurve,
         rawPeak = MET.area,
         rawIS = d6MET.area,
         nominal = MET.nominalmass,
         poly = "2nd",
         IDcol = SampleID,
         useNLS_outnames = FALSE)

# Using weights in the nonlinear regression
stdCurve(ExStdCurve,
         normPeak = MET.peakarearatio,
         nominal = MET.nominalmass,
         poly = "1st",
         weights = "1/x")

# Omitting certain points from the regression but showing them on the graph
stdCurve(ExStdCurve,
         normPeak = MET.peakarearatio,
         nominal = MET.nominalmass,
         poly = "2nd",
         omit = which(ExStdCurve$MET.nominalmass > 10 &
                            ExStdCurve$MET.nominalmass < 20),
         useNLS_outnames = FALSE)

# Coloring by some variable
stdCurve(ExStdCurve %>% dplyr::mutate(Group = c(rep("A", 5), rep("B", 6))),
         normPeak = MET.peakarearatio,
         nominal = MET.nominalmass,
         colorBy = Group,
         poly = "2nd")

shirewoman2/LaurasHelpers documentation built on Oct. 22, 2023, 2:07 p.m.