Allows for the re-computation of the differential status and re-plotting volcano and MA plot for each contrast.
reapply.thresholds(
DEprot.analyses.object,
linear.FC = 2,
p.adjusted = 0.05,
linear.FC.unresp.range = c(1/1.1, 1.1),
up.color = "indianred",
down.color = "steelblue",
unresponsive.color = "purple",
null.color = "gray"
)An object of class DEprot.analyses.
Number indicating the (absolute) fold change threshold (linear scale) to use to define differential proteins. Default: 2.
Numeric value indicating the p.adjusted threshold (or FDR threshold if analyses performed usinf prolfqua) to apply to the differential analyses. Default: 0.05.
A numeric 2-elements vector indicating the range (linear scale) used to define the unresponsive fold changes. Default: c(1/1.1, 1.1).
String indicating the color to use for up-regulated proteins in the plots. Default: "indianred".
String indicating the color to use for up-regulated proteins in the plots. Default: "steelblue".
String indicating the color to use for unresponsive proteins in the plots. Default: "purple".
String indicating the color to use for null proteins in the plots. Default: "gray".
An object of the same class than the input provided to the function.
dpo_analyses <- reapply.thresholds(DEprot::test.toolbox$diff.exp.limma,
linear.FC = 1.3, p.adjusted = 0.01)