Tutorial Notebook - Anderson-Lab/ComplementaryDomainPrioritization GitHub Wiki

source("http://bioconductor.org/biocLite.R")
biocLite("SSOAP",suppressUpdates=T)
biocLite("AnnotationDbi",suppressUpdates=T)
biocLite("GSEABase",suppressUpdates=T)
biocLite("Biostrings",suppressUpdates=T)
biocLite("KEGGREST",suppressUpdates=T)
install.packages('devtools',repos='http://cran.us.r-project.org')
library(devtools)
install_github("Anderson-Lab/ComplementaryDomainPrioritization")

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BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.0.
Installing package(s) 'SSOAP'



The downloaded source packages are in
	‘/tmp/RtmpA4Izum/downloaded_packages’


BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.0.
Installing package(s) 'AnnotationDbi'



The downloaded source packages are in
	‘/tmp/RtmpA4Izum/downloaded_packages’


BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.0.
Installing package(s) 'GSEABase'

library(ComplementaryDomainPrioritization)
download.example.data(allow.cache=F)

Loading required package: GSEABase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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    mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unlist, unsplit

Loading required package: Biobase
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    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
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Loading required package: annotate
Loading required package: AnnotationDbi
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Loading required package: GenomeInfoDb
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Attaching package: 'AnnotationDbi'

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Loading required package: KEGGREST


[1] "Downloading to ./Cattaneo_array.csv"
[1] "Downloading to ./Marra_0_kegg_protein_enrichment.tsv"
[1] "Downloading to ./Marra_0_tf_protein_enrichment.tsv"
[1] "Downloading to ./Marra_0_wiki_protein_enrichment.tsv"
[1] "Downloading to ./TCGA_protein.csv"
[1] "Downloading to ./TCGA_rna.csv"
[1] "Downloading to ./Uzozie_protein.csv"
[1] "Downloading to ./Marra_5percentFDR_tf_protein_enrichment.tsv"
[1] "Downloading to ./Marra_5percentFDR_wiki_protein_enrichment.tsv"
[1] "Downloading to ./Marra_5percentFDR_kegg_protein_enrichment.tsv"

file = "./Marra_5percentFDR_kegg_protein_enrichment.tsv"
kegg.pathways = load.WebGestalt(file,'Kegg')


head(kegg.pathways)

KEGGgene.ids = get.genes.kegg(kegg.pathways)

[1] "path:hsa03010"
[1] "path:hsa01100"
[1] "path:hsa03050"
[1] "path:hsa03040"
[1] "path:hsa00970"
[1] "path:hsa00640"
[1] "path:hsa05012"
[1] "path:hsa00190"
[1] "path:hsa00280"
[1] "path:hsa00010"
[1] "path:hsa05016"
[1] "path:hsa00620"
[1] "path:hsa04610"
[1] "path:hsa05010"
[1] "path:hsa04141"
[1] "path:hsa00520"
[1] "path:hsa00410"
[1] "path:hsa00360"
[1] "path:hsa00020"
[1] "path:hsa03013"
[1] "path:hsa00630"
[1] "path:hsa04260"
[1] "path:hsa03060"
[1] "path:hsa00380"
[1] "path:hsa00071"
[1] "path:hsa03450"
[1] "path:hsa00230"
[1] "path:hsa05100"
[1] "path:hsa00260"
[1] "path:hsa00500"
[1] "path:hsa00051"
[1] "path:hsa00270"
[1] "path:hsa00350"
[1] "path:hsa00310"
[1] "path:hsa00053"
[1] "path:hsa03018"
[1] "path:hsa00052"
[1] "path:hsa00030"



head(KEGGgene.ids)

file = "Cattaneo_array.csv"
Cattaneo.rna = load.gene.data(file,5)
KEGGprioritized.data = list.filter(Cattaneo.rna$transposed.data,KEGGgene.ids)


head(KEGGprioritized.data)