Quickly retrieve the sequences of a Biostrings object

Source: R/get.seqs.R

Helper function to retrieve the sequences of a Biostrings object.

get.seqs(object, type = "DNA")

Arguments

object

a Biostrings object.
type

either type = "DNA" or type = "AA".

Author

Hajk-Georg Drost

Examples

# read example sequences
seqs <- system.file("nt.fa",package = "LTRpred")
input.seqs <- Biostrings::readDNAStringSet(seqs)

# retrieve sequences of Biostrings object
head(get.seqs(input.seqs))
#> $`1_CHROMOSOME_dumped__149500_155909|-2:1718-2806(6410)`
#> 1089-letter DNAString object
#> seq: TAGGAGATTATGACTCATGAACGCGGCTATGATTTG...GAGATGGTTAAGGATCGAATTGTTTCACAAGGAAAT
#> 
#> $`1_CHROMOSOME_dumped__149500_155909|+1:1-1341(6410)`
#> 1341-letter DNAString object
#> seq: GGTTTCACCGTCACTTTCATCATCCCCGGCGATTCT...CAACGAAAGATCGACCAAGAACAGGAATCATTTCTA
#> 
#> $`1_CHROMOSOME_dumped__249531_259127|-2:1536-2222(9597)`
#> 687-letter DNAString object
#> seq: TAAAGATTATCGAAAACAATCTTCATACTCAAAATG...TTAATATGTTTTTATGGTAATTATTTAAGAAAATTT
#> 
#> $`1_CHROMOSOME_dumped__428932_438092|+2:4208-5056(9161)`
#> 849-letter DNAString object
#> seq: TAAAAACTTGCAACTTGCAAATACTCTTTTCCCCTC...GTCACGTATGTAAACAATATCCCTCGGGATTGGCTC
#> 
#> $`1_CHROMOSOME_dumped__3357954_3363283|-3:2674-3369(5330)`
#> 696-letter DNAString object
#> seq: TGATTTTGCTACAATTGTGGGAAGTTTGGACATTAT...AAGCAAGGTTGTGAAGTTGTATTCAAGTTTAAAGCA
#> 
#> $`1_CHROMOSOME_dumped__3357954_3363283|-2:326-1321(5330)`
#> 996-letter DNAString object
#> seq: TAAATGTCGGATGATCCTGGACAGATGTTGCTCATC...TCGTGGTCATGGGCACTACAGGTTTGTGGCACACTA
#>