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Dave Gerrard, University of Manchester

2011

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R scripts to analyse Cliff Rowe's Liver Protein dataset.

There is quite a bit of setting up of directories and R packages before running the scripts. It would be best to have the same version of R (or later?)

A master script called LiverProtsAnalysisMaster.R lists the other scripts and can be used to call them.

RUNNING THE SCRIPTS.

LiverProteins dependencies and packages.

SESSION INFO (these are the packages loaded by the end of the process.

sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32

locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252

attached base packages: [1] grid stats graphics grDevices utils datasets methods base

other attached packages: [1] org.Hs.eg.db_2.4.1 qvalue_1.24.0 gplots_2.8.0 caTools_1.10 bitops_1.0-4.1
[6] gdata_2.8.0 gtools_2.6.2 lattice_0.18-8 topGO_1.16.2 SparseM_0.88
[11] GO.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 AnnotationDbi_1.10.2 Biobase_2.8.0
[16] graph_1.28.0

loaded via a namespace (and not attached): [1] tcltk_2.11.1 tools_2.11.1

LIBRARIES

might be best to install bioconductor

source("http://bioconductor.org/biocLite.R")

biocLite()

install.packages(c("topGO", "lattice", "gplots", "qvalue", "org.Hs.eg.db")) # these may take some time.

explicitly loaded packages. These are loaded from the scripts.And need to have been installed

library(topGO) library(lattice) require(gplots) library(qvalue) library(org.Hs.eg.db)

may be a bunch of dependencies to do with BioConductor and topGO. e.g. GO.db, AnnotationDbi

INPUT FILES

baseProteinByLiverSample <- read.delim("C:/Users/dave/LiverProteins/data/Cliffs dataset.txt", header=T) prot2go <- readMappings("C:/Users/dave/LiverProteins/data/go2prot.map") expDesignLiverProteins <- read.delim("C:/Users/dave/LiverProteins/data/CliffsExpDesign.txt", header=T)

this kappaMatrix can be recalculated as part of the script

kappaMatrix <- read.delim("C:/Users/dave/LiverProteins/data/ubiProtsKappaMatrixDetected.tab",sep="\t",header=T)

See LiverProtsAnalysisMaster.R for individual scripts.