plot_detect: Visualize intensities of proteins with missing values
In arnesmits/DEP: Differential Enrichment analysis of Proteomics data

Description Usage Arguments Value Examples

plot_detect generates density and CumSum plots of protein intensities with and without missing values

1	plot_detect(se)

`se`	SummarizedExperiment, Data object with missing values.

Density and CumSum plots of intensities of proteins with and without missing values (generated by ggplot).

# 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
filt <- filter_missval(se, thr = 0)

# Plot intensities of proteins with missing values
plot_detect(filt)