propd Pairs by DE ResultsThe getColours function "colours" the pairs based on a
vector of differential expression (DE) results. If both members
in the pair are DE, the colour is "Green". If both members in the
pair are not DE, the colour is "Red". If only one is DE, the
colour is "Yellow". This allows the results of a DE analysis
to affect the interpretation of differential proportionality.
Importantly, the significance of differential proportionality is
independent of the DE method used.
getColours(object, DE, cutoff = NA, include = NA, or = TRUE)getColors(object, DE, cutoff = NA, include = NA, or = TRUE)
Any propd object.
A logical vector. The i-th element should state whether the i-th gene is differentially expressed.
For updateCutoffs, a numeric vector.
this argument provides the FDR cutoffs to test.
For graph functions, a numeric scalar. This argument
indicates the maximum theta to include in the figure.
For graph functions, a large integer will instead
retrieve the top N pairs as ranked by theta.
This argument indicates which features by
name should belong to a pair for that pair to get included
in the results. Subset performed by
Partner %in% subset | Pair %in% subset.
A boolean. If FALSE, include subsets
by Partner %in% subset & Pair %in% subset.
A data.frame. The output of getResults
with a "colour" column.
For use in conjunction with getNormTheta.