R/get_dataset.R
convert_to_biostrings.Rd
This function converts, when possible, a regulon_result object into a Biostrings object.
convert_to_biostrings(regulondb_result, seq_type = "DNA")
regulondb_result | A regulon_result object. |
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seq_type | A character string with either DNA or protein, specyfing what |
A XStringSet object.
Alejandro Reyes
## 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" ) ## Obtain all the information from the "GENE" dataset convert_to_biostrings(get_dataset(e_coli_regulondb, dataset = "GENE")) #> Warning: Dropped 2 entries where sequence data were NAs #> DNAStringSet object of length 4600: #> width seq #> [1] 1080 ATGCAAGCGGCAACTGTTGTGATTAACCGCCG...CTTCAAGGGTCGCGATGAAATACGTGGATTAA #> [2] 690 ATGATACTGACCGATCCAGAATGGCAGGCAGT...CCAGAATCAGCCGTGAACGGGCGGGGCGCTAA #> [3] 762 ATGGTTTCATCATTCACATCTGCCCCACGCAG...GCTATCGCGATAAACACGCGATGTGGCGGTAA #> [4] 1221 ATGAGCCTGGCCGGTAAAAAAATCGTTCTCGG...TGACCCGTTATGATGAAAAAAATCGACGTTAA #> [5] 1341 ATGTTATTTACTATCCAACTTATCATAATACT...GGATCTTCGCCGCGATGTACGGGTTCTTATAA #> ... ... ... #> [4596] 72 ATGATTAACCAAGTGAGCGTTTATCGACAACC...TGAGCGGATGCCGACAGGTAAAAACCATTTAA #> [4597] 66 ATGGAAACGTTCTGTTACATGAAATGGCCCGTTAGACATCACAAATCGCGAAGAGTTTCCCATTAA #> [4598] 90 ATGAATAACCCCGTCTGTCTTGATGACTGGTT...CTTTGGCCGTAATAGCTCTGCTAATAATATAA #> [4599] 150 ATGAGCCTCGTTTTATGCTTTTTGTTAATGTC...TGACCTTAATTGTCTTTTTAAATAAAAAATAA #> [4600] 101 ATATCTGTAATAAGAAATAGCCCTCGCCGCTT...ATGGTTGGCCATCGTATGATGGCCTTTTTTGT