Each column of a contrast matrix represents a pairwise comparison of all samples or cells of a grandR object (or a column annotation table). Elements being 1 are contrasted vs. elements being -1 (and all 0 are irrelevant for this comparison).
Arguments
- d
A grandR object or a column annotation table
- name
the name of the contrast
- A
definition of the condition of interest, see details
- B
definition of the reference condition , see details
Value
A data frame with a single column representig a contrast matrix to be used in ApplyContrasts, LFC, PairwiseDESeq2
Details
This creates a contrast A vs B (i.e. the fold change would be A/B)
Columns that belong to A or B can be given as a logical, integer or character vector representing a selection of the columns (samples or cells).
The expression is evaluated in an environment having the Coldata, i.e. you can use names of Coldata as variables to
conveniently build a logical vector (e.g., columns=Condition="x").