## ----LRBase.XXX.eg.db, echo=FALSE------------------------------------------ suppressPackageStartupMessages(library("LRBase.Hsa.eg.db")) ## ----LRBase.XXX.eg.db2, echo=TRUE------------------------------------------ columns(LRBase.Hsa.eg.db) keytypes(LRBase.Hsa.eg.db) key_HSA <- keys(LRBase.Hsa.eg.db, keytype="GENEID_L") head(select(LRBase.Hsa.eg.db, keys=key_HSA[1:2], columns=c("GENEID_L", "GENEID_R"), keytype="GENEID_L")) ## ----LRBase.XXX.eg.db3, echo=TRUE------------------------------------------ lrPackageName(LRBase.Hsa.eg.db) lrNomenclature(LRBase.Hsa.eg.db) species(LRBase.Hsa.eg.db) lrListDatabases(LRBase.Hsa.eg.db) lrVersion(LRBase.Hsa.eg.db) dbInfo(LRBase.Hsa.eg.db) dbfile(LRBase.Hsa.eg.db) dbschema(LRBase.Hsa.eg.db) dbconn(LRBase.Hsa.eg.db) ## ----LRBase.XXX.eg.db4, echo=TRUE------------------------------------------ suppressPackageStartupMessages(library("RSQLite")) dbGetQuery(dbconn(LRBase.Hsa.eg.db), "SELECT * FROM DATA WHERE GENEID_L = '9068' AND GENEID_R = '14' LIMIT 10") ## ----LRBaseDbi, echo=FALSE------------------------------------------------- suppressPackageStartupMessages(library("LRBaseDbi")) ## ----LRBaseDbi2, echo=TRUE------------------------------------------------- example("makeLRBasePackage") ## ----scTensor, echo=FALSE-------------------------------------------------- suppressPackageStartupMessages(library("scTensor")) suppressPackageStartupMessages(library("SingleCellExperiment")) suppressPackageStartupMessages(library("MeSH.Hsa.eg.db")) ## ----cellCellSetting, fig.cap="Germline, Male, GSE86146", echo=TRUE, fig.width=10, fig.height=10---- data(GermMale) data(labelGermMale) data(tsneGermMale) sce <- SingleCellExperiment(assays=list(counts = GermMale)) reducedDims(sce) <- SimpleList(TSNE=tsneGermMale$Y) plot(reducedDims(sce)[[1]], col=labelGermMale, pch=16, cex=2, xlab="Dim1", ylab="Dim2", main="Germline, Male, GSE86146") legend("topleft", legend=c(paste0("FGC_", 1:3), paste0("Soma_", 1:4)), col=c("#9E0142", "#D53E4F", "#F46D43", "#ABDDA4", "#66C2A5", "#3288BD", "#5E4FA2"), pch=16) ## ----scTensor2, echo=FALSE------------------------------------------------- suppressPackageStartupMessages(library("LRBase.Mmu.eg.db")) suppressPackageStartupMessages(library("MeSH.Mmu.eg.db")) ## ----cellCellDecomp2, echo=TRUE-------------------------------------------- cellCellSetting(sce, LRBase.Hsa.eg.db, labelGermMale, names(labelGermMale)) ## ----cellCellDecomp, echo=TRUE--------------------------------------------- cellCellDecomp(sce, ranks=c(2,3,4)) ## ----cellCellRank, echo=TRUE----------------------------------------------- (rks <- cellCellRanks(sce)) rks$selected ## ----sessionInfo, echo=FALSE----------------------------------------------- sessionInfo()