## ----风格，回声=假，结果='ASIS'-------------------------- - knitr：：opts_chunk $ set（eval = as.logical（sys.getenv（“knitr_eval”，“true”）），cache = as.logical（sys.getenv（“knitr_cache”，“true”））选项（宽度= 75）## ----消息=假-------------------------------------------------图书馆（enrichmentbrowser）## ----消息= false，回声= false -------------------------------------图书馆（DESEQ2）库（Airway）库（Dopltr）库（Org.hs.eg.db）库（Go.db）库（Limma）## ---------------------------------------------------------------图书馆（气道）数据（气道）Airway $ Dex < - Ententel（Airway $ Dex，“Untrt”）##------------------------------------------------------------------------------------------图书馆（deseq2）des < - deseqdataset（呼吸道，设计=〜cell + dex）des < - deseq（des）res < -结果（des）## -----------------------------------------------------------------------------------------------------------------------图书馆（dibble）图书馆（tibble）tbl < - res％>％as.data.frame（）％rownames_to_column（“Ensembl") %>% as_tibble() tbl ## ------------------------------------------------------------------------ library(org.Hs.eg.db) tbl <- tbl %>% mutate( ENTREZID = mapIds( org.Hs.eg.db, ENSEMBL, "ENTREZID", "ENSEMBL" ) %>% unname() ) tbl ## ------------------------------------------------------------------------ tbl <- tbl %>% filter(!is.na(padj), !is.na(ENTREZID)) tbl ## ------------------------------------------------------------------------ library(limma) go <- goana(tbl$ENTREZID[tbl$padj < .05], tbl$ENTREZID, "Hs") %>% as_tibble() ## ------------------------------------------------------------------------ library(GO.db) go <- go %>% mutate( GOID = mapIds( GO.db, .$Term, "GOID", "TERM" ) %>% unname() ) %>% dplyr::select(GOID, everything()) %>% arrange(P.DE) ## ------------------------------------------------------------------------ go %>% filter(grepl("glucocorticoid", Term)) ## ------------------------------------------------------------------------ genesets <- AnnotationDbi::select(org.Hs.eg.db, tbl$ENTREZID, "GO", "ENTREZID") %>% as_tibble() %>% dplyr::select(ENTREZID, GO, ONTOLOGY) %>% distinct() genesets ## ------------------------------------------------------------------------ sessionInfo()