E14TG2a: LOPIT experiment on Mouse E14TG2a Embryonic Stem Cells from...

In lgatto/pRolocdata: Data accompanying the pRoloc package

LOPIT experiment on Mouse E14TG2a Embryonic Stem Cells from Breckels et al. (2016)

Description

This is data from a standard LOPIT experimental design on Mouse E14TG2a embryonic stem cells. See below for more details.

Usage

data(E14TG2aS1)
data(E14TG2aS2)
data(E14TG2aR)
data(E14TG2aS1yLoc)
data(E14TG2aS1goCC)

Format

The data is an instance of class MSnSet from package MSnbase.

Details

This is a LOPIT experiment. Normalised intensities of proteins from eight iTRAQ 8-plex labelled fractions are available for 2 replicates (indexed 1 and 2) using stringent and relaxed setting (S and R, respectively).

The E14TG2aS1goCC instance contains binary assay data. Its columns represent GO CC terms that have been observed for the object's features. A 1 indicates that a GO term has been associated to a given feature (protein); a 0 means not such association was found in the GO ontology.

The E14TG2aS1yLoc instance contains 34 sequence and annotation features obtained from a feature selection of the sequence and annotation features from the computational classifier YLoc. These features include: variants of psuedo amino acid counts, autocorrelation, sum of charge, prosite patterns, Gene Ontoloy terms and the number of signal peptides. These features are described in detail in Breckels et al (2015).

Source

The data was generated by A. Christoforou at the Cambridge Centre for Proteomics, Cambridge. http://www.bio.cam.ac.uk/proteomics/.

Examples

data(E14TG2aS1)
E14TG2aS1
pData(E14TG2aS1)
head(exprs(E14TG2aS1))

lgatto/pRolocdata documentation built on Oct. 17, 2024, 10:16 p.m.