plot_detect {DEP} | R Documentation

## Visualize intensities of proteins with missing values

### Description

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

### Usage

    plot_detect(se)

### Arguments

`se` | SummarizedExperiment, Data object with missing values.

### Value

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

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

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

[Package DEP version 1.8.0 Index]