## ---------- echo = true -----------------------------------------------------------------------------------------------------------------------------------------库（“ AnnotationHub”）AH <-AnnotationHub（）McOLS（AH）## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------dbfile <-query（ah，c（“ lrbasedb”，“ homo sapiens”，“ v002”））[[1]] ## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ - - - - - - - - - - - - - - - - - - - - - - - 图书馆（"LRBaseDbi") LRBase.Hsa.eg.db <- LRBaseDbi::LRBaseDb(dbfile) ## ----Access, echo=TRUE---------------------------------------------------------------------列（lrbase.hsa.eg.db）keytypes（lrbase。（“ geneid_l”，“ geneid_r”），keytype =“ geneid_l”）## ------------------------------------------------------------------------- lrnomenclature（lrbase.hsa.eg.db）物种（lrbase.hsa。例如.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) ## ----Other2, echo=TRUE-------------------------------------------------------- suppressPackageStartupMessages(library("RSQLite")) dbGetQuery(dbconn(LRBase.Hsa.eg.db), "SELECT * FROM DATA WHERE GENEID_L = '9068' AND GENEID_R = '14' LIMIT 10") ## ----SCE1, echo=TRUE---------------------------------------------------------- suppressPackageStartupMessages(library("scTensor")) suppressPackageStartupMessages(library("SingleCellExperiment")) ## ----SCE2, 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$Y) plot(reducedDims(sce)[[1]], col=labelGermMale, pch=16, cex=2, xlab="Dim1", ylab="Dim2", main="Germline, Male, GSE86146") legend("topleft", legend=c(paste0("FGC_", 1:3), paste0("Soma_", 1:4)), col=c("#9E0142", "#D53E4F", "#F46D43", "#ABDDA4", "#66C2A5", "#3288BD", "#5E4FA2"), pch=16) ## ----cellCellSetting, echo=TRUE----------------------------------------------- cellCellSetting(sce, LRBase.Hsa.eg.db, names(labelGermMale)) ## ----cellCellDecomp, echo=TRUE------------------------------------------------ set.seed(1234) cellCellDecomp(sce, ranks=c(2,3)) ## ----cellCellRank, echo=TRUE-------------------------------------------------- (rks <- cellCellRanks(sce)) rks$selected ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()