get_dna_objects {regutools} | R Documentation |
Retrieve genomic elements from regulonDB
get_dna_objects( regulondb, genome = "eschColi_K12", grange = GRanges("chr", IRanges(1, 5000)), elements = "gene" )
regulondb |
A |
genome |
A valid UCSC genome name. |
grange |
A |
elements |
A character vector specifying which annotation elements to
plot. It can be any from: |
GenomicRanges::GRanges-class()
object with the elements found.
Joselyn Chavez
## Connect to the RegulonDB database if necessary if (!exists("regulondb_conn")) { regulondb_conn <- connect_database() } ## Build the regulondb object e_coli_regulondb <- regulondb( database_conn = regulondb_conn, organism = "chr", database_version = "1", genome_version = "1" ) ## Get all genes from E. coli get_dna_objects(e_coli_regulondb) ## Get genes providing Genomic Ranges grange <- GenomicRanges::GRanges( "chr", IRanges::IRanges(5000, 10000) ) get_dna_objects(e_coli_regulondb, grange) ## Get aditional elements within genomic positions get_dna_objects(e_coli_regulondb, grange, elements = c("gene", "promoter") )