add_nsaf: Normalize protein abundances by 'NSAF'

In DanielSprockett/reltools: Microbiome Amplicon Analysis and Visualization

Description

normalizes proteome data by a Normalized Spectral Abundance Factor using the protein length as specified by the length parameter in the tax_table of a phyloseq object The input otu_table should contain proteomic count or intensity values from a mass spec.

Usage

add_nsaf(ps, length)

Arguments

ps	A phyloseq object that contains a tax_table. The tax_table must contain protein length as specified with the length parameter.
length	A column in the tax_table containing the protein length.

Value

This function returns the input phyloseq object with a the otu_table() normalized by NSAF. The Normalized Spectral Abundance Factor was proposed by Zybailov et al. (2006). NSAF for a protein 'k' is the number of spectral counts ('SpC', the total number of MS/MS spectra) identifying a protein, 'k', divided by the protein<e2><80><99>s length ('L'), divided by the sum of 'SpC'/'L' for all 'N' proteins in the experiment.

Examples

ps <- add_nsaf(ps)

DanielSprockett/reltools documentation built on May 5, 2019, 12:27 p.m.