## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", # quietly = TRUE)) { # install.packages("BiocManager") # } # BiocManager::install("SynExtend") ## ----build_synteny_object----------------------------------------------------- library(SynExtend) DBPATH <- system.file("extdata", "Endosymbionts.sqlite", package = "SynExtend") Syn <- FindSynteny(dbFile = DBPATH) ## ----synplots01--------------------------------------------------------------- Syn pairs(Syn) ## ----synplots02--------------------------------------------------------------- print(head(Syn[[1, 2]])) print(head(Syn[[2, 1]])) ## ----generate_genecalls------------------------------------------------------- # generating genecalls with local data: GC <- gffToDataFrame(GFF = system.file("extdata", "GCF_021065005.1_ASM2106500v1_genomic.gff.gz", package = "SynExtend"), Verbose = TRUE) # in an effort to be space conscious, not all original gffs are kept within this package GeneCalls <- get(data("Endosymbionts_GeneCalls", package = "SynExtend")) ## ----print_gene_calls--------------------------------------------------------- print(head(GeneCalls[[1]])) ## ----show_rtracklayer, eval = FALSE------------------------------------------- # X01 <- rtracklayer::import(system.file("extdata", # "GCA_000875775.1_ASM87577v1_genomic.gff.gz", # package = "SynExtend")) # class(X01) # print(X01) ## ----generate_initial_links--------------------------------------------------- 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()