hikaku.itrap	R Documentation
Process label-free comparative proteomics data

Description

This function returns comparative log2 ratio analysis and mean peak area heatmap comparison from label-free proteomics or an exploratory graphical sample data analysis.

Usage

hikaku.itrap("data.csv", samplen, nrep, ...)
Arguments

data.csv	
A tab-delimited .csv file in Protein Discoverer (ThermoLife) output format.
samplen	
A natural number >1 and <16 for samples/conditions
nrep	
A natural number >0 for replicates of each sample/condition
expl	
TRUE for exploratory analysis and FALSE for comparative label-free proteomics analysis. Default: expl=FALSE
pep	
A natural number for a threshold of the minimal number of peptides detected. Default: pep=0
psm	
A natural number for a threshold of minimal PSM value. Default:psm=0
heat.qt	
A rational number (0<x<1) which means the fraction of upper quantile to not appear in the heatmap. Default:heat.qt=0.1
pnames	
TRUE for protein id as names and FALSE for Accession number. Default:pnames=TRUE
housek	
Accession number with "" for the housekeeping protein selected for internal sample normalization
Author(s)

Tiago A. de Souza (tiagoantonio@gmail.com)
Fernando G. de Almeida (fernandoalmeida@usp.br)