## ----style, echo=FALSE, results='asis', message=FALSE-------------------- BiocStyle::markdown() ## ----评估= false ---------------------------------------------------------------------------------------------------------------------------------------------------------＃install.packages（“ Biocmanager”）＃Biocmanager :: install（“ AnnotationHub”）## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------库（'AnnotationHub'）＃创建AnnotationHub连接AH <-AnnotationHub（）＃搜索所有eupathdb资源meta <-query（ah，“ eupathdb”）长度（meta）head（meta）＃EUPATHDB数据可用表（META $ rdataclass）＃通过特定数据库表（Meta $ dataProvider）进行资源分配＃资源可用长度（唯一（元（Meta $ thert））头的生物列表＃------------------------------------------------------------------------------------------------------------ res < - 查询（ah，c（'Leishmania Major Friedlin'，'orgdb'，'eupathdb'））Res＃＃＃---------------------------------------------------------------------------------------------------------- orgdb <-Res [['ah65089']]类（orgdb）## ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃列出可用的字段以检索列（orgdb）＃创建一个包含有机体GID的所有基因ID的向量<-keys（orgdb，keytype ='gid'）head（gids）＃检索每个基因dat <-section的染色体，描述和生物型（orgdb，keys = gids，keytype ='gid ='gid'，columns = c（'chr'，'type'，'geneDescription'））head（dat）表（dat $ type）表（dat $ chr）＃创建基因 / go术语gene_go_mapping gene_go_mapping <-选择（orgdb，keys = gids，keytype =''gid'，列= c（'go_id'，'go_term_name'，'notology'））head（gene_go_mapping）＃reterieve kegg等。路径注释gene_pathway_mapping_mapping <-选择（orgdb，keys，keys = gids = gids = gids，keytype ='gid ='gid'，列，列，列，列= c（'pathway'，'pathway_source'））表（gene_pathway_mapping $ pathway_source）head（gene_pathway_mapping）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # query AnnotationHub res< - 查询（ah，c（'Leishmania Major Friedlin'，'Granges'，'eupathdb'）））））） res # retrieve a GRanges instance associated with the result record gr <- res[['AH65354']] gr ## ------------------------------------------------------------------------ # chromosome names seqnames(gr) # strand information strand(gr) # feature widths width(gr) ## ------------------------------------------------------------------------ # list of location types in the resource table(gr$type) ## ------------------------------------------------------------------------ # get the first three ranges gr[1:3] # get all gene entries on chromosome 4 gr[gr$type == 'gene' & seqnames(gr) == 'LmjF.04'] ## ------------------------------------------------------------------------ sessionInfo()