Normalize: Normalization

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

Description

This function offers several modes of normalization to correct for different sources of error, and enables calculating differential protein expression and stoichiometry of post-tranlsational modification even from sparsely annotated datasets.

Usage

Normalize(data, iso.norm = NA, equim.iso.norm = NA, internal.norm = NA,
  tot.current = F, mod)

Arguments

data	data frame with 12 columns as decribed in documentation.
iso.norm	takes a character string corresponding to the reference isotopologue to which the other isotopologue will be normalized (e.g. iso.norm = "H"). The string must match the corresponding annotation in the "Label" column.
equim.iso.norm	takes a character string corresponding to the reference isotopologue to which the other isotopologue will be normalized (e.g. iso.norm = "H"). The string must match the corresponding annotation in the "Label" column.
internal.norm	takes in a vector of character strings corresponding to the peptide sequence of the reference peptides to which other peptides are normalized (e.g. internal.norm = "ATDVIVP"). If more than one reference peptide is indicated (e.g. internal.norm = c("ATDVIVP","AAATDVI")), a geometric mean of the corresponding intensity values is taken. This normalization equalizes the intensities for the specified peptides in each sample.
tot.current	takes in a boolean input indicating whether or not normalization to total ion current is to be made (e.g. tot.current = T). This normalization equalizes the sum of all intensities in each sample, used as a proxy for total ion current.
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.

Value

data frame of normalized data

Examples

Normalize(testData,tot.current = T,mod="Phosphorylation")

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