add_rejections {DEP} | R Documentation

## Mark significant proteins

### Description

`add_rejections` marks significant proteins based on defined cutoffs.

### Usage

    add_rejections(diff, alpha = 0.05, lfc = 1)

### Arguments

`diff` | SummarizedExperiment, Proteomics dataset on which differential enrichment analysis has been performed (output from `test_diff()`).
`alpha` | Numeric(1), Sets the threshold for the adjusted P value.
`lfc` | Numeric(1), Sets the threshold for the log2 fold change.

### Value

A SummarizedExperiment object annotated with logical columns indicating significant proteins.

### Examples

    # Load example
    data <- UbiLength
    data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",]
    data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

    # Make SummarizedExperiment
    columns <- grep("LFQ.", colnames(data_unique))
    exp_design <- UbiLength_ExpDesign
    se <- make_se(data_unique, columns, exp_design)

    # Filter, normalize and impute missing values
    filt <- filter_missval(se, thr = 0)
    norm <- normalize_vsn(filt)
    imputed <- impute(norm, fun = "MinProb", q = 0.01)

    # Test for differentially expressed proteins
    diff <- test_diff(imputed, "control", "Ctrl")
    dep <- add_rejections(diff, alpha = 0.05, lfc = 1)

[Package DEP version 1.9.0 Index]