LOPIT data sets used in Trotter et al. 2010.

Description

The two Arabidobsis LOPIT data sets trotter2010shallow and trotter2010steep have been used in Trotter et al. (2010) to illustrate improvement of sub-cellular resolution upon data fusion. The data have originally been published in Dunkley et al. (2006) and Sadowski et al. (2008), respectively.

Usage

data(trotter2010shallow)
data(trotter2010steep)

Format

The data are instances of class MSnSet from package MSnbase.

Source

Supporting information available on http://onlinelibrary.wiley.com/doi/10.1002/pmic.201000359/abstract

References

Trotter MWB, Sadowski PG, Dunkley TPJ, Groen AJ and Lilley KS. Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Proteomics 2010 10(23):4213-4219. PMID 21058340.

Sadowski PG, Groen AJ, Dupree P and Lilley KS. Sub-cellular localization of membrane proteins. Proteomics 2008 8(19):3991-4011. PMID 18780351.

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

library(pRoloc)
## Replication of figure 4 from Trotter et al.
## individual data sets
data(trotter2010steep)
data(trotter2010shallow)
## combined data
combined <- combine(trotter2010shallow,
                    trotter2010steep)
par(mfrow = c(1,3))
plot2D(trotter2010shallow, fcol = "TAIR8", main = "Shallow")
plot2D(trotter2010steep, fcol = "TAIR8", main = "Steep")
plot2D(combined, fcol = "TAIR8", main = "Combined")
addLegend(combined, where = "bottomleft",
          fcol = "TAIR8", bty = "n", ncol = 2)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(pRolocdata)
Loading required package: MSnbase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

The following object is masked from 'package:stats':

    smooth

The following object is masked from 'package:base':

    trimws


This is pRolocdata version 1.10.0.
Use 'pRolocdata()' to list available data sets.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pRolocdata/trotter2010.Rd_%03d_medium.png", width=480, height=480)
> ### Name: trotter20010
> ### Title: LOPIT data sets used in Trotter et al. 2010.
> ### Aliases: trotter20010 trotter2010steep trotter2010shallow
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(pRoloc)
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
Loading required package: cluster

This is pRoloc version 1.12.4 
  Read '?pRoloc' and references therein for information
  about the package and how to get started.

> ## Replication of figure 4 from Trotter et al.
> ## individual data sets
> data(trotter2010steep)
> data(trotter2010shallow)
> ## combined data
> combined <- combine(trotter2010shallow,
+                     trotter2010steep)
> par(mfrow = c(1,3))
> plot2D(trotter2010shallow, fcol = "TAIR8", main = "Shallow")
> plot2D(trotter2010steep, fcol = "TAIR8", main = "Steep")
> plot2D(combined, fcol = "TAIR8", main = "Combined")
> addLegend(combined, where = "bottomleft",
+           fcol = "TAIR8", bty = "n", ncol = 2)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>