# #——style-knitr eval = TRUE,呼应= FALSE,结果= "飞机 "-------------------- BiocStyle:乳胶 () ## ---- 预赛,回声= FALSE --------------------------------------------- ## FIXME: 邻接矩阵——w。颜色+ / - 1 # # FIXME: limma topTable——> GeneColorSet # # w . verbose = TRUE suppressPackageStartupMessages({库(GSEABase)库(hgu95av2.db)库(GO.db ) }) ## ---- GeneSet --------------------------------------------------------------- 数据(sample.ExpressionSet) #从Biobase egs < GeneSet(样本。ExpressionSet 201:250,, setName =) egs # #——geneIds“样本” --------------------------------------------------------------- 头(geneIds (egs )) ## ---- 细节 --------------------------------------------------------------- 细节(egs ) ## -------------------------------------------------------------------------- ## FIXME: GeneSet (AnnotationIdentifier(“hgu95av2”))——>非空# # FIXME:GeneSet (AnnotationIdentifier(“hgu95av2”),# # collectionType = GOCollection())过滤GOCollection(或KEGG) # #——GeneSet-methods ------------------------------------------------------- showMethods(“GeneSet”,继承了= FALSE) # #——GeneIdentifierTypes --------------------------------------------------- 名称(槽(getClass(“GeneIdentifierType”)、“子类 ")) ## ---- mapIdentifiers -------------------------------------------------------- mapIdentifiers (egsEntrezIdentifier ()) ## ---- GeneSet_Identifiers --------------------------------------------------- 库(注释)# getEG开斋节< -独特(getEG (geneIds (egs),“hgu95av2”))<——开斋节开斋节[! is.na(宰牲节)]GeneSet (EntrezIdentifier (), geneIds = as.character(宰牲节 )) ## ---- CollectionType -------------------------------------------------------- 名称(槽(getClass(“CollectionType”),“子类 ")) ## ---- GOCollection ---------------------------------------------------------- GeneSet (GOCollection (c(“去:0005488”,“去:0019825”),evidenceCode =“艾达”),geneIdType = EntrezIdentifier(“org.Hs.eg.db”),setName = "样本集合 ") ## ---- 广泛的 ----------------------------------------------------------------- fl < -系统。文件(“extdata”、“Broad1.xml”、包=“GSEABase”)英国地质调查局< - GeneSet (BroadCollection (), url = fl)英国地质调查局# #——Broad-to-annotation --------------------------------------------------- bgs1 < - mapIdentifiers(英国地质调查局AnnotationIdentifier(“hgu95av2”))bgs1 # #——子集 ---------------------------------------------------------------- 英国地质调查局[1:5]英国地质调查局[c(“GALNS”,“LOC646365 ")] ## ---- egs-bgs --------------------------------------------------------------- egs & bgs1 # #——subset-ExpressionSet -------------------------------------------------- 样本。ExpressionSet[bgs，] ## ----GeneColorSet-setup, echo=FALSE, results="hide"------------------------ conn <- textConnection(" Entrez ID，基因符号，表达水平，表型响应##过去是MRP2 1244, ABCC2，增加，抗性538,ATP7A，增加，抗性540,ATP7B，增加，抗性9961,MVP，增加，抗性##下面的LRP必须是MVP ##LRP，增加，抗性-需要知道哪个7507,XPA，增加，抗性2067,ERCC1，增加，抗性##TOP，增加，耐-需要知道哪一个，笔记说II 672, BRCA1，增加，耐3725,JUN，增加，耐#GCS，增加，耐-我的笔记说阿尔法-GCS -所以哪一个?##我只发现伽玛在PubMed作为相关2730,GCLM，增加，抵抗”)tbl <- read.csv(conn, strip。白色= TRUE,发表评论。char="#", stringsAsFactors = TRUE) 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)