Mark significant proteins
DEP2_add_rejections.Rdadd_rejections marks significant proteins based on defined cutoffs.
Usage
# S4 method for SummarizedExperiment
add_rejections(diff, alpha, lfc, thresholdmethod, curvature, x0_fold)
# S4 method for DEGdata
add_rejections(diff, alpha, lfc, thresholdmethod, curvature, x0_fold)Arguments
- alpha
Numeric(1), Sets the threshold for the adjusted P value.
- lfc
Numeric(1), Sets the threshold for the log2 fold change.
- thresholdmethod
Character(1), The thresholdmethod to decide significant.should be one of "intersect" ,"curve". If thresholdmethod = "curve", cutoff lines is the curves with function y = c/(x-x0). c is the curvature, and x0 is the minimum fold change which relatived to the standard deviations of L2FC distribution
- curvature
Numeric(1), Sets the curvature for the curve cutoff lines
- x0_fold
Numeric(1), decide the x0 ratio to the standard deviations of L2FC. The x0 usually is set to 1(medium confidence) or 2(high confidence) standard deviations.