get_results: Generate a results table

In squirrelandr/DEP: Differential Enrichment analysis of Proteomics data

Description

get_results generates a results table from a proteomics dataset on which differential enrichment analysis was performed.

Usage

get_results(dep)

Arguments

dep	SummarizedExperiment, Data object for which differentially enriched proteins are annotated (output from test_diff() and add_rejections()).

Value

A data.frame object containing all results variables from the performed analysis.

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)

# Get results
results <- get_results(dep)
colnames(results)

significant_proteins <- results[results$significant,]
nrow(significant_proteins)
head(significant_proteins)

squirrelandr/DEP documentation built on May 7, 2019, 9:31 a.m.