import_IsobarQuant: Import from IsobarQuant

In arnesmits/DEP: Differential Enrichment analysis of Proteomics data

Description

import_IsobarQuant imports a protein table from IsobarQuant and converts it into a SummarizedExperiment object.

Usage

import_IsobarQuant(proteins, expdesign, intensities = "signal_sum",
  names = "gene_name", ids = "protein_id", delim = "[|]")

Arguments

proteins	Data.frame, Protein table for which unique names will be created.
expdesign	Data.frame, Experimental design with 'label', 'condition' and 'replicate' information. See UbiLength_ExpDesign for an example experimental design.
intensities	Character(1), Prefix of the columns containing sample intensities.
names	Character(1), Name of the column containing feature names.
ids	Character(1), Name of the column containing feature IDs.
delim	Character(1), Sets the delimiter separating the feature names within on protein group.

Value

A SummarizedExperiment object with log2-transformed values and "name" and "ID" columns containing unique names and identifiers.

Examples

## Not run: 
# Load data
isobarquant_table <- read.csv("testfile.txt", header = TRUE,
                              stringsAsFactors = FALSE, sep = "\t")
exp_design <- read.csv("test_experimental_design.txt", header = TRUE,
                              stringsAsFactors = FALSE, sep = "\t")
# Import data
se <- import_IsobarQuant(isabarquant_table, exp_design)


## End(Not run)

arnesmits/DEP documentation built on Aug. 7, 2019, 10:44 a.m.