proteusLabelFree: Proteus example label free data

In bartongroup/proteusLabelFree: Example label-free data set for proteus package

Description

Example data set for proteus package. It comes from a label-free MS/MS experiment in two biological conditions (called A and B) and seven replicates each. The data come from an unpublished experiment by Katharina Trunk, Sarah Coulthurst, Julien Peltier and Matthias Trost.

Format

Nine objects from different stages of data processing:

evi

Pre-processed evidence data (data frame)

meta

Metadata (data frame)

meta.clean

Clean metadata (data frame)

pepdat

Peptide data (proteusData object)

pepdat.clean

Clean peptide data (proteusData object)

prodat

Protein data (proteusData object)

annotations

Protein annotations downloaded from UniProt

annotations.id

Protein annotations ready for merging

evitab.example

Example fragment of evidence data

This package also contains the full original evidence file, peptides file, proteinGroups file and formatted metadata file (see examples below).

Examples

library(proteusLabelFree)
data(proteusLabelFree)
meta
head(pepdat$tab)
head(prodat$tab)

evidenceFile <- system.file("extdata", "evidence.txt.gz", package="proteusLabelFree")
peptidesFile <- system.file("extdata", "peptides.txt.gz", package="proteusLabelFree")
proteinGroupsFile <- system.file("extdata", "proteinGroups.txt.gz", package="proteusLabelFree")
metadataFile <- system.file("extdata", "metadata.txt", package="proteusLabelFree")

bartongroup/proteusLabelFree documentation built on June 23, 2020, 7:53 a.m.