## ---------------------------------------------------------------------------------------------------------------------------＃if（！sireseenamespace（“ biocmanager”，＃seetly = true））{＃install.packages（“ biocmanager”）＃}＃biocmanager：biocmanager：：install（“ synextend”）## ---- build_synteny_object -------------------------------------------------------------------------------------------------------------------------------------------------------------库（synextend）dbpath <-system.file（“ extdata”，“ endosymbionts.sqlite”，package =“ synextend”）syn <-FindSynteny（dbfile = =dbpath）## ----- synplots01 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------印刷（SYN（SYN）[[1，2]）））打印（head（syn [[2，1]]））## ---- generate_geneCalls -----------------------------------------------------------------------------------------------------------------------------------------＃与本地数据生成基因：GC <-gfftodataframe（gff = system。file（“ extdata”，“ gcf_021065005.1_asm2106500v1_genomic.gff.gz”，package =“ synextend”），verbose = true）kage genecalls < - get（data（“ endosymbionts_genecalls”，package =“ synextend”））## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- print(head(GeneCalls[[1]])) ## ----show_rtracklayer, eval = FALSE------------------------------------------ # X01 <-rtracklayer :: import（system.file（“ extdata”，＃“ GCA_000875775.1_ASM875777V1_GENOMIC.GFF.GZ”，＃package =“ synextend”）＃class（x01）＃class（x01）＃------------------------------------------------------------------------------------ Links <- NucleotideOverlap(SyntenyObject = Syn, GeneCalls = GeneCalls, Verbose = TRUE) ## ---- link_printing----------------------------------------------------------- class(Links) print(Links) ## ---- describe_links---------------------------------------------------------- LinkedPairs1 <- PairSummaries(SyntenyLinks = Links, DBPATH = DBPATH, PIDs = FALSE, Verbose = TRUE) ## ---- describe_more_links_again----------------------------------------------- print(head(LinkedPairs1)) ## ---- pairsummariesoperations------------------------------------------------- SingleLinkageClusters <- DisjointSet(Pairs = LinkedPairs1, Verbose = TRUE) ## ---- clusters---------------------------------------------------------------- # extract the first 10 clusters Sets <- ExtractBy(x = LinkedPairs1, y = DBPATH, z = SingleLinkageClusters[1:10], Verbose = TRUE) head(Sets) ## ----------------------------------------------------------------------------- sessionInfo()