pairwise_LFQ: Pairwise label-free quantitation: convert MaxQuant...

In devradiumking/maxabpp: Visualization of MaxQuant output for activity-based protein profiling experiments

Description

Pairwise label-free quantitation: convert MaxQuant modificationSpecificPeptides.txt file to a volcano plot-ready table

Usage

pairwise_LFQ(
  raw = read_tsv("modificationSpecificPeptides.txt"),
  metadata = read_tsv("metadata.txt"),
  name_probe_mod,
  max_each_mod = 1,
  max_total_mods = 1,
  quantitation_level = "peptide",
  background_check = FALSE,
  normalize_to = NULL
)

Arguments

raw	a dataframe by reading modificationSpecificPeptides.txt
metadata	a dataframe that maches the MaxQuant input. Column 1: Intensity (such as Intensity samplename, same as the column names in modificationSpecificPeptides.txt) name Column 2: Replicate group (use the same name for each group of replicates)
name_probe_mod	a string vector of chemical probe/modification names, such as c("Mod1", "Mod2"), must match MaxQuant input
max_each_mod	a integer as the maximal number of modifications on a single peptide, set for each chemical probe
max_total_mods	a integer as the maximal number of modifications on a single peptide, set for all chemical probes Note max_each_mod must not be less than max_total_mods
quantitation_level	a string, must be either "peptide" or "protein"
background_check	a boolean, FALSE = quantify probe-modified peptides, TRUE = quantify non-probe-modified peptides
normalize_to	a string, must be either "sum_all", "mean_all", (normalize to all peptides) "sum_background", or "mean_background" (normalize to background/non-probe-modified peptides).

Value

a dataframe table of peptides, proteins and their corresponding -log10(p-value) and log2(FC)

Examples

output <- pairwise_LFQ(raw = read.delim("modificationSpecificPeptides.txt", header=TRUE, sep="\t"), metadata = read.delim("metadata.txt", header=TRUE, sep="\t"), name_probe_mod = c("Mod1", "Mod2"), max_each_mod = 1, max_total_mods = 1, quantitation_level = "peptide" , background_check = FALSE, normalize_to = "mean_all")

devradiumking/maxabpp documentation built on May 31, 2020, 9:01 a.m.