STEPP_Ligand.Fun: STEPP Ligand Analysis

In amkeele2/DukeProteomicsSuite: Pipeline for Proteomic Energetic Methods

Description

This function will take STEPP/LiP (TMT10plex) data directly from ProteomeDiscoverer (v. 2.3) and generate a volcano plot and hit list based on user-defined SD and p-values

Usage

STEPP_Ligand.Fun(
  STEPP_Raw,
  SD_cutoff = 2,
  p_cutoff = 0.05,
  TMTplex = 10,
  plot = TRUE,
  xlab = "Z Score",
  ylab = "- log10 (p value)",
  labelcolor = c("grey", "red"),
  alpha = 0.5,
  plottextsize = 12,
  correctedpvalue = FALSE,
  interactiveplot = FALSE
)

Arguments

SD_cutoff	A positive integer (default = 2)
p_cutoff	A positive integer between 0 and 1 (default = 0.05)
TMTplex	8, 10, 16 TMTplex (default = 10)
plot	Display volcano plot (default = TRUE)
xlab	X-axis Label (default = "Z Score")
ylab	Y-axis Label (default = "- log10 (p value)")
labelcolor	Color of Not significant and Significant data points (default = c("grey", "red"))
alpha	Transparency of plot (default = 0.5)
plottextsize	Text Size of plot (default = 12)
correctedpvalue	Bonferroni corrected p-value (default = FALSE)
interactiveplot	Plotly interactive Volcano plot (default = FALSE)
Expression_data	Raw ProteomeDiscoverer (v. 2.3) data
TPP_data	Raw STEPP (TMT10plex) ProteomeDiscoverer (v. 2.3) data

Value

Volcano plot, Hit list, Total proteins assayed and Unique protein hits

amkeele2/DukeProteomicsSuite documentation built on April 27, 2021, 6:41 a.m.