at_chloro: The AT_CHLORO data base

In lgatto/pRolocdata: Data accompanying the pRoloc package

The AT_CHLORO data base

Description

AT_CHLORO is a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins.

The assayData contains the raw spectral counts for 3 chloroplastic fractions (the envelope, the stroma and the thylakoids) and for a complete chloroplast sample. The percentage of occurrence in each of the sub-chloroplast fraction as calculated in Ferro et al. (2010) are available as feature meta data (Percent_ENV, Percent_STR and Percent_THY).

Usage

data(at_chloro)

Format

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

Source

Myriam Ferro Exploring the Dynamics of Proteomes (EDyP) Laboratoire Biologie a Grande Echelle (BGE) U1038 INSERM/CEA/UJF Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV) CEA/Grenoble

References

Ferro M, Brugiere S, Salvi D, Seigneurin-Berny D, Court M, Moyet L, Ramus C, Miras S, Mellal M, Le Gall S, Kieffer-Jaquinod S, Bruley C, Garin J, Joyard J, Masselon C, Rolland N. AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins. Mol Cell Proteomics. 2010 Jun;9(6):1063-84. Epub 2010 Jan 10. PubMed PMID: 20061580; PubMed Central PMCID: PMC2877971

Examples

data(at_chloro)
dim(at_chloro)
pData(at_chloro)
head(exprs(at_chloro))
fvarLabels(at_chloro)
table(fData(at_chloro)$markers)
## check exprs data and 'TotalSpectralCount' feature meta data
all(fData(at_chloro)$TotalSpectralCount == rowSums(exprs(at_chloro)))
## create a set with the percentage of occurrence, as in Ferro et al. 2010
## rows that have no 'TOT' in the feature vars of interest
sel <- apply(fData(at_chloro)[, c("Percent_ENV", "Percent_STR", "Percent_THY")],
             1, function(.x) length(grep("TOT", .x)) == 0)
## new MSnSet
at_chloro2 <- at_chloro[sel, 1:3]
## columns of interest
perc <- c("Percent_ENV", "Percent_STR", "Percent_THY")                                        
## create a new intensity matrix
exprs2 <-  matrix(as.numeric(as.matrix(fData(at_chloro2)[, perc])), ncol
= 3)
colnames(exprs2) <- sampleNames(at_chloro2)
rownames(exprs2) <- featureNames(at_chloro2)
summary(rowSums(exprs2))
exprs(at_chloro2) <- exprs2
validObject(at_chloro2)

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