createContrast: Create contrast matrix

In diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

Description

Create contrast matrix for differential testing

Usage

createContrast(contrast)

Arguments

contrast

Vector defining the contrast of interest. This should be a numeric vector specifying the combination of model parameters to test whether they are equal to zero. The entries correspond to the columns of the design matrix, or the levels of the fixed effect terms in the model formula. For example, using a design matrix: c(0, 1, 0, 0, 0) to test whether a single parameter corresponding to the second column in the design matrix is equal to zero.

Details

Creates a contrast matrix specifying the comparison of interest, in the correct format for the differential testing functions. This can then be provided to the differential testing functions, together with either a design matrix or model formula, and the data object.

The argument contrast defines the contrast of interest. This should be a numeric vector specifying the combination of model parameters to test whether they are equal to zero. In many cases, this will simply be a vector of zeros and a single entry equal to one; this will test whether a single parameter is equal to zero (e.g. c(0, 1, 0, 0, 0)).

If a design matrix has been used, the entries of contrast correspond to the columns of the design matrix; and the length of contrast equals the number of columns in the design matrix. If a model formula has been used, the entries correspond to the levels of the fixed effect terms; and the length equals the number of levels of the fixed effect terms.

The contrast matrix is formatted as a matrix with a single column containing the contrast of interest. To perform tests for multiple contrasts, run this function and the corresponding differential testing function multiple times.

Value

contrast: Returns a contrast matrix containing the contrast of interest, formatted as a matrix with a single column.

Examples

# For a complete workflow example demonstrating each step in the 'diffcyt' pipeline, 
# see the package vignette.

# Example: contrast matrix
createContrast(c(0, 1, 0, 0, 0))

diffcyt documentation built on Nov. 8, 2020, 6:37 p.m.