Function to convert output of regulondb queries to Biostrings objects

Source: R/get_dataset.R

This function converts, when possible, a regulon_result object into a Biostrings object.

convert_to_biostrings(regulondb_result, seq_type = "DNA")

Arguments

regulondb_result

A regulon_result object.

seq_type

A character string with either DNA or protein, specyfing what

Value

A XStringSet object.

Author

Alejandro Reyes

Examples

## Connect to the RegulonDB database if necessary
if (!exists("regulondb_conn")) regulondb_conn <- connect_database()

## 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