R/get_binding_sites.R
get_binding_sites.Rd
Retrieve the binding sites and genome location for a given transcription factor.
get_binding_sites(regulondb, transcription_factor, output_format = "GRanges")
regulondb | A |
---|---|
transcription_factor | name of the transcription factor. |
output_format | The output object. Can be either a |
Either a GRanges object or a Biostrings object summarizing information about the binding sites of the transcription factors.
José Alquicira Hernández, Jacques van Helden, Joselyn Chávez
## Connect to the RegulonDB database if necessary if (!exists("regulondb_conn")) regulondb_conn <- connect_database() #> snapshotDate(): 2021-10-20 ## Build the regulon db object e_coli_regulondb <- regulondb( database_conn = regulondb_conn, organism = "E.coli", database_version = "1", genome_version = "1" ) ## Get the binding sites for AraC get_binding_sites(e_coli_regulondb, transcription_factor = "AraC") #> GRanges object with 15 ranges and 1 metadata column: #> seqnames ranges strand | #> <Rle> <IRanges> <Rle> | #> ECK120015742-araB-araC E.coli 70110-70126 + | #> ECK120012328-araB-araC E.coli 70131-70147 + | #> ECK120012320-araB-araC E.coli 70184-70200 - | #> ECK120012323-araB-araC E.coli 70205-70221 - | #> ECK120012603-araB-araC E.coli 70342-70358 - | #> ... ... ... ... . #> ECK120012333-araF E.coli 1986396-1986412 - | #> ECK120012915-araE E.coli 2982244-2982260 - | #> ECK120012913-araE E.coli 2982265-2982281 - | #> ECK125108641-xylA E.coli 3730824-3730840 - | #> ECK125108643-xylA E.coli 3730847-3730863 - | #> sequence #> <character> #> ECK120015742-araB-araC ataaaaagcgTCAGGTAGGA.. #> ECK120012328-araB-araC ccgctaatctTATGGATAAA.. #> ECK120012320-araB-araC tctataatcaCGGCAGAAAA.. #> ECK120012323-araB-araC caaaaacgcgTAACAAAAGT.. #> ECK120012603-araB-araC attcagagaaGAAACCAATT.. #> ... ... #> ECK120012333-araF ccaaagacaaCAAGGATTTC.. #> ECK120012915-araE tccatatttaTGCTGTTTCC.. #> ECK120012913-araE cgacatgtcgCAGCAATTTA.. #> ECK125108641-xylA taacataattGAGCAACTGA.. #> ECK125108643-xylA attatctcaaTAGCAGTGTG.. #> ------- #> seqinfo: 1 sequence from an unspecified genome; no seqlengths