createContrast {diffcyt} | R Documentation |
Create contrast matrix for differential testing
createContrast(contrast)
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. For example, |
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 most cases, this will simply be a vectors 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 length of contrast
should be equal to the
number of columns in the design matrix. If a model formula has been used, the length of
contrast
should equal the number of 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.
contrast
: Returns a contrast matrix containing the contrast of interest,
formatted as a matrix with a single column.
# 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))