nikolovski2012: Meta-analysis from Nikolovski et al. (2012)

In lgatto/pRolocdata: Data accompanying the pRoloc package

Meta-analysis from Nikolovski et al. (2012)

Description

This is the data used in Nikolovksi et al. (2012). See below for details and references.

Usage

data(nikolovski2012)
data(nikolovski2012imp)

Format

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

Details

These data are a concatenation of 4 LOPIT experiments. Experiments 1 and 2 are from Dunkley et al. 2006 (see also dunkley2006). Exepriments 3 and 4 are new.

In the LOPIT experiments by Dunkley et al. (2006), peripheral membrane proteins were removed by carbonate washing of the isolated membranes, while for experiments 3 and 4, no carbonate wash was performed and are, as such, enriched in peripheral and luminal proteins. See figure 1 in Nikolovski 2012 for a description of the design.

In nikolovksi2012imp missing values have been imputed using partial least-squares regression.

The training set used for the Naive Bayesian classifier is available as the markers feature meta-data. Note that Nikolovksi included a group of markers labelled 'others', which has been retained in these data sets. The results produced in this work are available in the preds feature variable (note that some organelles are marked with a '*', which is undefined here).

Source

Supporting Information on http://www.plantphysiol.org/content/160/2/1037.long, also available in the package's extdata directory.

References

Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P. Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. Plant Physiol. 2012 Oct;160(2):1037-51. doi: 10.1104/pp.112.204263. Epub 2012 Aug 24. PMID: 22923678; PMCID: PMC3461528.

Dunkley TP, Hester S, Shadforth IP, Runions J, Weimar T, Hanton SL, Griffin JL, Bessant C, Brandizzi F, Hawes C, Watson RB, Dupree P, Lilley KS. Mapping the Arabidopsis organelle proteome. Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6518-23. Epub 2006 Apr 17. PubMed PMID: 16618929; PubMed Central PMCID: PMC1458916.

Examples

data(nikolovski2012)
data(nikolovski2012imp)
table(is.na(nikolovski2012))
table(is.na(nikolovski2012imp))
phenoData(nikolovski2012)
table(fData(nikolovski2012)$markers)
all.equal(sort(featureNames(nikolovski2012)),
          sort(featureNames(nikolovski2012imp)))
library("pRoloc")
plot2D(nikolovski2012imp)
addLegend(nikolovski2012imp, where = "topright", bty = "n", cex =.7)

lgatto/pRolocdata documentation built on April 7, 2023, 1:56 a.m.