Analyze: Analyze

In kentsisresearchgroup/ProteoModlR: R Suite for Quantitative Proteomics Pathway Modeling

Description

This function calculates peptides site occupancy and/or abundance.

Usage

Analyze(data, mod, stoich = "", abund = "", ref.state = NA)

Arguments

data	data frame with 12 columns as decribed in documentation. Output of Normalize function
mod	If any chemoform of a given peptide bears the modification specified in mod="" (f.ex. mod="phosphorylation") all peptides with the same sequence and containing the modification will be classified as Modified, while all peptides with the same sequence and not containing the modification will be classified as Not-Modified. If none of the chemoforms of a peptide contains the specified modification, the peptide is classified Abundance.
stoich	user's preference for calculating the site occupancy of peptides for which either calculations are possible. Possible arguments: "Exact" or "Approximate".
ref.state	option to normalize to a reference condition (e.g. ref.state="Disease").
adund	user's preference for exact or approximate abundance calculations. Possible arguments: "Exact" or "Approximate".

Value

data frame of analyzed data

Examples

normalized <- Normalize(testData,tot.current = T,mod="Phosphorylation")
Analyze(data=normalized,mod="Phosphorylation",stoich="Exact")

kentsisresearchgroup/ProteoModlR documentation built on May 20, 2019, 9:05 a.m.