Description Usage Arguments Details Value Examples
View source: R/createContrast.R
Create contrast matrix for differential testing
1  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. 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:

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.
contrast
: Returns a contrast matrix containing the contrast of interest,
formatted as a matrix with a single column.
1 2 3 4 5  # 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))

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