artmsVolcanoPlot {artMS} | R Documentation

## Volcano plot (log2fc / pvalues)

### Description

It generates a scatter-plot used to quickly identify changes

### Usage

    artmsVolcanoPlot(
      mss_results,
      output_name = "volcano_plot.pdf",
      lfc_upper = 1,
      lfc_lower = -1,
      whatPvalue = "adj.pvalue",
      FDR = 0.05,
      PDF = TRUE,
      decimal_threshold = 16,
      verbose = TRUE
    )

### Arguments

`mss_results` | (data.frame or file) Selected MSstats results
`output_name` | (char) Name for the output file (don't forget the `.pdf` extension)
`lfc_upper` | (numeric) log2fc upper threshold (positive value)
`lfc_lower` | (numeric) log2fc lower threshold (negative value)
`whatPvalue` | (char) `pvalue` or `adj.pvalue` (default)
`FDR` | (numeric) False Discovery Rate threshold
`PDF` | (logical) Option to generate pdf format. Default: `T`
`decimal_threshold` | (numeric) Decimal threshold for the pvalue. Default: 16 (10^-16)
`verbose` | (logical) `TRUE` (default) shows function messages

### Value

(pdf) of a volcano plot

### Examples

    artmsVolcanoPlot(mss_results = artms_data_ph_msstats_results,
                      whatPvalue = "pvalue",
                      PDF = FALSE)

[Package artMS version 1.10.2 Index]