getColours: Label 'propd' Pairs by DE Results

In propr: Calculating Proportionality Between Vectors of Compositional Data

Description

The 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.

Usage

getColours(object, DE, cutoff = NA, include = NA, or = TRUE)

getColors(object, DE, cutoff = NA, include = NA, or = TRUE)

Arguments

object	Any propd object.
DE	A logical vector. The i-th element should state whether the i-th gene is differentially expressed.
cutoff	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.
include	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.
or	A boolean. If FALSE, include subsets by Partner %in% subset & Pair %in% subset.

Details

For use in conjunction with getNormTheta.

Value

A data.frame. The output of getResults with a "colour" column.

propr documentation built on Dec. 16, 2019, 9:30 a.m.