artmsVolcanoPlot: Volcano plot (log2fc / pvalues)

In kroganlab/artMS: Analytical R tools for Mass Spectrometry

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)

kroganlab/artMS documentation built on July 7, 2023, 5:35 a.m.