getLocationsAndScales: Calculate Location and Scale

In ClassifyR: A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Description

Calculates the location and scale for each feature.

Usage

  ## S4 method for signature 'matrix'
getLocationsAndScales(measurements, ...)
  ## S4 method for signature 'DataFrame'
getLocationsAndScales(measurements, location = c("mean", "median"),
                      scale = c("SD", "MAD", "Qn"))
  ## S4 method for signature 'MultiAssayExperiment'
getLocationsAndScales(measurements, targets = names(measurements), ...)

Arguments

measurements	Either a matrix, DataFrame or MultiAssayExperiment containing the data. For a matrix, the rows are features, and the columns are samples.
targets	If measurements is a MultiAssayExperiment, the names of the data tables to be used. "clinical" is also a valid value and specifies that numeric variables from the clinical data table will be used.
...	Variables not used by the matrix nor the MultiAssayExperiment method which are passed into and used by the DataFrame method.
location	The type of location to be calculated.
scale	The type of scale to be calculated.

Details

"SD" is used to represent standard deviation and "MAD" is used to represent median absolute deviation.

Value

A list of length 2. The first element contains the location for every feature. The second element contains the scale for every feature.

Author(s)

Dario Strbenac

References

Qn: http://www.tandfonline.com/doi/pdf/10.1080/01621459.1993.10476408

Examples

  genesMatrix <- matrix(rnorm(1000, 8, 4), ncol = 10)
  distributionInfo <- getLocationsAndScales(genesMatrix, "median", "MAD")
  
  mean(distributionInfo[["median"]]) # Typical median.
  mean(distributionInfo[["MAD"]]) # Typical MAD.

ClassifyR documentation built on Nov. 8, 2020, 6:53 p.m.