Identification of differentially abundant peptide/protein

This function allows to identify differentially abundant peptide/protein

Usage

is.differential(pvalue, logFC, thpvalue, thlogFC)

Arguments

pvalue: A vector of p-values.
logFC: A vector of logFC.
thpvalue: A float indicating the p-value threshold.
thlogFC: A float indicating the logFC threshold.

Value

A vector indicating which peptide/protein is differentially abundant (1) or not (0).

Author

Manon Gaudin

Examples

data(subR25prot)
obj <- subR25prot
# Simulate imputation
obj <- NAIsZero(obj, 1)
obj <- NAIsZero(obj, 2)
allComp <- limmaCompleteTest(
SummarizedExperiment::assay(obj[[length(obj)]]), 
design.qf(obj), 
comp.type="OnevsOne")
is.differential(allComp$P_Value[, 1], allComp$logFC[, 1], 0.05, 0.5)
#>   [1] 0 0 1 1 0 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#>  [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 1 0 1 1 0 1 0 0 1 0 0 0
#>  [75] 0 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0