## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex() ## ----preliminaries, echo=FALSE--------------------------------------------- ## FIXME: adjacency matrix -- color w. +/- 1 ## FIXME: limma topTable --> GeneColorSet ## w. verbose=TRUE suppressPackageStartupMessages({ library(GSEABase) library(hgu95av2.db) library(GO.db) }) ## ----GeneSet--------------------------------------------------------------- data(sample.ExpressionSet) # from Biobase egs <- GeneSet(sample.ExpressionSet[201:250,], setName="Sample") egs ## ----geneIds--------------------------------------------------------------- head(geneIds(egs)) ## ----details--------------------------------------------------------------- details(egs) ## -------------------------------------------------------------------------- ## FIXME: GeneSet(AnnotationIdentifier("hgu95av2")) --> non-empty ## FIXME: GeneSet(AnnotationIdentifier("hgu95av2"), ## collectionType=GOCollection()) filters on GOCollection (or KEGG) ## ----GeneSet-methods------------------------------------------------------- showMethods("GeneSet", inherited=FALSE) ## ----GeneIdentifierTypes--------------------------------------------------- names(slot(getClass("GeneIdentifierType"), "subclasses")) ## ----mapIdentifiers-------------------------------------------------------- mapIdentifiers(egs, EntrezIdentifier()) ## ----GeneSet_Identifiers--------------------------------------------------- library(annotate) # getEG eids <- unique(getEG(geneIds(egs), "hgu95av2")) eids <- eids[!is.na(eids)] GeneSet(EntrezIdentifier(), geneIds=as.character(eids)) ## ----CollectionType-------------------------------------------------------- names(slot(getClass("CollectionType"), "subclasses")) ## ----GOCollection---------------------------------------------------------- GeneSet(GOCollection(c("GO:0005488", "GO:0019825"), evidenceCode="IDA"), geneIdType=EntrezIdentifier("org.Hs.eg.db"), setName="Sample GO Collection") ## ----Broad----------------------------------------------------------------- fl <- system.file("extdata", "Broad1.xml", package="GSEABase") bgs <- GeneSet(BroadCollection(), urls=fl) bgs ## ----Broad-to-annotation--------------------------------------------------- bgs1 <- mapIdentifiers(bgs, AnnotationIdentifier("hgu95av2")) bgs1 ## ----subset---------------------------------------------------------------- bgs[1:5] bgs[c("GALNS", "LOC646365")] ## ----egs-bgs--------------------------------------------------------------- egs & bgs1 ## ----subset-ExpressionSet-------------------------------------------------- sample.ExpressionSet[bgs,] ## ----GeneColorSet-setup, echo=FALSE, results="hide"------------------------ conn <- textConnection(" Entrez ID, Gene Symbol, Expression level, Phenotype response ##used to be MRP2 1244, ABCC2, Increase, Resistant 538, ATP7A, Increase, Resistant 540, ATP7B, Increase, Resistant 9961, MVP, Increase, Resistant ##the LRP below must be MVP ##LRP, Increase, Resistant - need to know which one 7507,XPA, Increase, Resistant 2067, ERCC1, Increase, Resistant ##TOP, Increase, Resistant - need to know which one, notes say II 672, BRCA1, Increase, Resistant 3725, JUN, Increase, Resistant #GCS, Increase, Resistant - my notes say alpha-GCS - so which one? ##I only found gamma at PubMed as being related 2730, GCLM, Increase, Resistant") tbl <- read.csv(conn, strip.white=TRUE, comment.char="#") close(conn) unlink(conn) ## ----GeneColorSet-phenotype------------------------------------------------ tbl ## ----GeneColorSet-constructor---------------------------------------------- gcs <- GeneColorSet(EntrezIdentifier(), setName="A color set", geneIds=as.character(tbl$Entrez.ID), phenotype="Cisplatin resistance", geneColor=tbl$Expression.level, phenotypeColor=tbl$Phenotype.response) gcs ## ----GeneSetCollection----------------------------------------------------- gsc <- GeneSetCollection(sample.ExpressionSet[201:250,], setType=GOCollection()) gsc gsc[["GO:0005737"]] ## ----GeneSetCollection-GOCollection---------------------------------------- GeneSetCollection(sample.ExpressionSet[201:300,], setType=GOCollection(evidenceCode="IMP")) ## ----GeneSetCollection-BroadCollection------------------------------------- ## FIXME: BroadCollection default to paste("c", 1:4, sep="") ## FIXME: GeneSetCollection(BroadCollection(), urls=fl); filters on bcCategory fl <- system.file("extdata", "Broad.xml", package="GSEABase") gss <- getBroadSets(fl) gss names(gss) ## ----mapIds-GeneSetCollection---------------------------------------------- gsc <- mapIdentifiers(gsc, EntrezIdentifier()) gsc gsc[["GO:0005737"]] ## ----ReportingTools-------------------------------------------------------- ## 'interesting' gene sets idx <- sapply(gsc, function(x) length(geneIds(x))) > 2 library(ReportingTools) gscReport <- HTMLReport( shortName="gsc_example", title="GSEABase Vignette GeneSetCollection", basePath=tempdir()) publish(gsc[idx], gscReport, annotation.db="org.Hs.eg") url <- finish(gscReport) ## ----ReportingTools-view, eval=FALSE--------------------------------------- # browseURL(url)