Project: Exemplary functions and report templates
In immunoassay: Functions for working with immunoassay data.

Description Usage Arguments Details Author(s) See Also

In addition to general utility and batch processing functions, the immunoassay library allows for creating nicely formatted reports. The reports are actually a separate, customizable Sweave scripts that can define their own R functions or utilize the vast array of functions already available in R. There are two LaTeX report templates included in this library: "example.run-report.R" and "example.project-report.R". Additionally, there are two functions utilized by these templates: project.means and project.qcplot function.

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project.means(x)
project.qcplot(x, samples=c("ConA","ConB"), type="pred", 
    breaks=c(1,length(unique(x$ID))), log=FALSE, ...)

`x`	A `data.frame` of results from the `batch` function - either `immunoassay.environment$l.run` or `immunoassay.environment$results`.
`samples`	Character vector of sample names to be plotted. A new plot will be called for each sample, so make sure to include `par(mfrow=)` parameter when using more than one sample in this place. This serves the purpose of having multiple plots on a single pdf page. Sample names must match the names in the data. The default is `c("ConA","ConB")`.
`type`	Character. This is the prefix of the column name in the data, that is followed by the analyte name. Currently this can have the following values: `"pred"` - selects predictions from the model (calculated values); `"MFI"` - selects MFI values for plotting; or `"CTS"` - selects counts (useless).
`breaks`	Numeric vector of "breaks" for the calculation and display of `mean` and `sd` bands on the plot. Useful for projects that utilized more than one kit lot number, to separate results from different kits. Must be provided manually - currently no automatic selection of kits is implemented.
`log`	Logical. If `TRUE`, the function takes a natural logarithm of y-axis values. Defaults to `FALSE`.
`...`	Other parameters passed along to `plot`.

The two functions mentioned above are simple utility functions called by the EXAMPLE report templates. These templates can be found in the "templates" folder of the immunoassay package, along with "Sweave.sty" LaTeX style. These templates are "Sweaved" in the process of batch-processing of immunoassay data using the batch function. These files should be copied to the main project folder on the user's computer and modified according to user's needs.

Michal J. Figurski, PhD mfigrs@gmail.com of the Biomarker Research Laboratory, University of Pennsylvania, Philadelphia, PA.

immunoassay, read.multiplex, read.kits and sigfit.

immunoassay documentation built on May 2, 2019, 4:45 p.m.