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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.