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() } #> snapshotDate(): 2021-10-20 ## 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) #> GRanges object with 3 ranges and 4 metadata columns: #> seqnames ranges strand | id type name #> <Rle> <IRanges> <Rle> | <character> <character> <character> #> [1] chr 337-2799 + | ECK120000987 gene thrA #> [2] chr 2801-3733 + | ECK120000988 gene thrB #> [3] chr 190-255 + | ECK120001251 gene thrL #> description #> <character> #> [1] fused aspartate kina.. #> [2] homoserine kinase #> [3] <i>thr</i> operon le.. #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengths ## Get genes providing Genomic Ranges grange <- GenomicRanges::GRanges( "chr", IRanges::IRanges(5000, 10000) ) get_dna_objects(e_coli_regulondb, grange) #> GRanges object with 3 ranges and 4 metadata columns: #> seqnames ranges strand | id type name #> <Rle> <IRanges> <Rle> | <character> <character> <character> #> [1] chr 337-2799 + | ECK120000987 gene thrA #> [2] chr 2801-3733 + | ECK120000988 gene thrB #> [3] chr 190-255 + | ECK120001251 gene thrL #> description #> <character> #> [1] fused aspartate kina.. #> [2] homoserine kinase #> [3] <i>thr</i> operon le.. #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengths ## Get aditional elements within genomic positions get_dna_objects(e_coli_regulondb, grange, elements = c("gene", "promoter") ) #> GRanges object with 19 ranges and 4 metadata columns: #> seqnames ranges strand | id type #> <Rle> <IRanges> <Rle> | <character> <character> #> [1] chr 337-2799 + | ECK120000987 gene #> [2] chr 2801-3733 + | ECK120000988 gene #> [3] chr 190-255 + | ECK120001251 gene #> [4] chr 148 + | ECK120010236 promoter #> [5] chr 38 + | ECK125230824 promoter #> ... ... ... ... . ... ... #> [15] chr 3066 + | ECK125230834 promoter #> [16] chr 3368 + | ECK125230835 promoter #> [17] chr 3396 + | ECK125230836 promoter #> [18] chr 3401 + | ECK125230837 promoter #> [19] chr 4241 + | ECK125230838 promoter #> name description #> <character> <character> #> [1] thrA fused aspartate kina.. #> [2] thrB homoserine kinase #> [3] thrL <i>thr</i> operon le.. #> [4] thrLp promoter with .. thrLp promoter with .. #> [5] TSS_1 promoter with .. TSS_1 promoter with .. #> ... ... ... #> [15] TSS_12 promoter with.. TSS_12 promoter with.. #> [16] TSS_13 promoter with.. TSS_13 promoter with.. #> [17] TSS_14 promoter with.. TSS_14 promoter with.. #> [18] TSS_15 promoter with.. TSS_15 promoter with.. #> [19] TSS_16 promoter with.. TSS_16 promoter with.. #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengths