trotter2010: LOPIT data sets used in Trotter et al. (2010)

In lgatto/pRolocdata: Data accompanying the pRoloc package

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.

The feature metadata contains the cellular compartment from TAIR8 and the pRoloc Arabidopsis markers (see pRolocmarkers).

Usage

data(trotter2010)
data(trotter2010shallow)
data(trotter2010steep)

Format

The data are instances of class MSnSet from package MSnbase. trotter2010 corresponds to the combined steep and shallow data.

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.

Examples

library(pRoloc)
## Replication of figure 4 from Trotter et al.
## individual data sets
data(trotter2010)
data(trotter2010steep)
data(trotter2010shallow)

par(mfrow = c(2,3))
plot2D(trotter2010shallow, fcol = "TAIR8", main = "Shallow (TAIR8)")
plot2D(trotter2010steep, fcol = "TAIR8", main = "Steep (TAIR8)")
plot2D(trotter2010, fcol = "TAIR8", main = "Combined (TAIR8)")
addLegend(trotter2010, where = "bottomleft", fcol = "TAIR8", ncol = 2)
plot2D(trotter2010shallow, main = "Shallow (markers)")
plot2D(trotter2010steep, main = "Steep (markers)")
plot2D(trotter2010, main = "Combined (markers)")
addLegend(trotter2010, where = "bottomleft", ncol = 2)

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