itzhak2017: Data from Itzhak et al. 2017

In lgatto/pRolocdata: Data accompanying the pRoloc package

Data from Itzhak et al. 2017

Description

The data from Itzhal et al. 2017 defines a spatial map for mouse primary neurons. The data are composed of 5 spatial maps, each containing 6 differential centrifugation fraction (as described in Itzhak et al. 2016, see itzhak2016stcSILAC).

The annotatied marker proteins are available in the itzhak2017markers dataset.

This data corresponds to the Mouse neuron Intensity and LFQ data data from supplemental table S3 (Proteomic Mouse Neuron Data Generated in This Study, Related to Figure 5).

Usage

data(itzhak2017)
data(itzhak2017markers)

Format

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

References

Itzhak DN, Davies C, Tyanova S, Mishra A, William son J, Antrobus R, Cox J, Weekes MP, Borner GHH. A Mass Spectrometry-Based Approach for Mapping Protein Subcellular Localization Reveals the Spatial Proteome of Mouse Primary Neurons. Cell Rep. 2017 Sep 12;20(11):2706-2718. doi: 10.1016/j.celrep.2017.08.063. PubMed PMID: 28903049; PubMed Central PMCID: PMC5775508.

Examples

data(itzhak2017)
itzhak2017

## experimental design
table(pData(itzhak2017))

## the expression data
exprs(itzhak2017)[1:5, 1:5]

## abstract
abstract(itzhak2017)

## split data by samples
x <- split(itzhak2017, "map")

## plotting
library("pRoloc")
par(mfrow = c(2, 3))
for (i in 1:5)
    plot2D(x[[i]], main = paste("Map", i))
plot2D(itzhak2017, main = "All maps")
addLegend(itzhak2017, where = "bottomleft")

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