calc_mp: Calculate mp-values

In lucyleeow/CellProfileR: Analyse Cell Morphology Data Generated By CellProfiler

Description

Calculate multidimensional perterbation value (mp-value) as described in Hutz et al.. Briefly, the mp-value can be used to determine whether any two treatments differ from each other and is similar in spirit to the p-value. This function was written by Hutz *et al.*.

Minor changes to the code and additional comments added are identified by a 'LL' next to the change.

Usage

calc_mp(dataset, txlabels, batchlabels, datacols, negctrls,
  allbyall = FALSE, dirprefix, outfile = "all_mp-values.txt",
  loadingsout = FALSE, pcaout = FALSE, gammaout = FALSE)

Arguments

dataset	Dataframe containing all data where each row is a sample and each columns is a feature/variable.
txlabels	Name of the column containing the treatment labels, as string. Each desired treatment group should have a unique label, within each batch (e.g. a treatment can have the same label in each batch as long as within one batch, the label uniquely identifies the treatment).
batchlabels	Name of the column containing the batch labels, as string
datacols	Vector of the column indicies that contain the feature/variable data to be used for calculating the mp-value.
negctrls	The name of the negative controls, in the 'txlabels' column, as string.
allbyall	Logical indicating whether to do all treatment-treatment comparisons (TRUE) or only treatment-control comparisons.
dirprefix	Path to the directory to store results in, as string. Do not include the trailing '/' at the end. This path will be created if it does not already exist.
outfile	Name of the file to save all the mp-values, as string.
loadingsout	Logical indicating whether the PCA loadings (eigenvectors) should be output.
pcaout	Logical indicating whether to output PCA values.
gammaout	Logical indicating whether to output gamma distribution parameters, p-value of goodness of fit and sample p-value according to the fit distribution. NOTE: When gammaout=TRUE, warnings like these may be displayed:

lucyleeow/CellProfileR documentation built on May 21, 2019, 2:30 a.m.