Creates sq object from object of class
from another package. Currently supported packages are ape,
bioseq, Bioconductor and seqinr. For exact list of
supported classes and resulting types, see details.
import_sq(object, ...)[any(1)]
An object of one of supported classes.
further arguments to be passed from or to other methods.
A tibble with sq column of
sq type representing the same sequences as given
object; the object has a type corresponding to the input type; if given
sequences have names, output tibble will also have
another column name with those names
Currently supported classes are as follows:
ape:
AAbin - imported as ami_bsc
DNAbin - imported as dna_bsc
alignment - exact type is guessed within sq
function
bioseq:
bioseq_aa - imported as ami_ext
bioseq_dna - imported as dna_ext
bioseq_rna - imported as rna_ext
Biostrings:
AAString - imported as ami_ext with exactly one
sequence
AAStringSet - imported as ami_ext
DNAString - imported as dna_ext with exactly one
sequence
DNAStringSet - imported as dna_ext
RNAString - imported as rna_ext with exactly one
sequence
RNAStringSet - imported as rna_ext
BString - imported as unt with exactly one
sequence
BStringSet - imported as unt
XStringSetList - each element of a list can be imported as
a separate tibble, resulting in a list of tibbles;
if passed argument separate = FALSE, these tibbles are bound into
one bigger tibble
seqinr:
SeqFastaAA - imported as ami_bsc
SeqFastadna - imported as dna_bsc
Providing object of class other than specified will result in an error.
Functions from input module:
random_sq(),
read_fasta(),
sq()
# ape example
library(ape)
#>
#> Attaching package: ‘ape’
#> The following object is masked from ‘package:tidysq’:
#>
#> complement
ape_dna <- as.DNAbin(list(one = c("C", "T", "C", "A"), two = c("T", "G", "A", "G", "G")))
import_sq(ape_dna)
#> # A tibble: 2 × 2
#> name sq
#> <chr> <dna_bsc>
#> 1 one CTCA <4>
#> 2 two TGAGG <5>
# bioseq example
library(bioseq)
#>
#> Attaching package: ‘bioseq’
#> The following objects are masked from ‘package:tidysq’:
#>
#> read_fasta, write_fasta
bioseq_rna <- new_rna(c(one = "ANBRY", two = "YUTUGGN"))
#> Warning: Non-standard IUPAC symbols detected for RNA: 1 characters were converted to N.
import_sq(bioseq_rna)
#> # A tibble: 2 × 2
#> name sq
#> <chr> <rna_ext>
#> 1 one ANBRY <5>
#> 2 two YUNUGGN <7>
# Biostrings example
library(Biostrings)
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#>
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:parallel’:
#>
#> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#> clusterExport, clusterMap, parApply, parCapply, parLapply,
#> parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following objects are masked from ‘package:dplyr’:
#>
#> combine, intersect, setdiff, union
#> The following object is masked from ‘package:tidysq’:
#>
#> paste
#> The following objects are masked from ‘package:stats’:
#>
#> IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#>
#> Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#> as.data.frame, basename, cbind, colnames, dirname, do.call,
#> duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#> lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#> pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#> tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> Loading required package: stats4
#>
#> Attaching package: ‘S4Vectors’
#> The following objects are masked from ‘package:dplyr’:
#>
#> first, rename
#> The following objects are masked from ‘package:base’:
#>
#> I, expand.grid, unname
#> Loading required package: IRanges
#>
#> Attaching package: ‘IRanges’
#> The following objects are masked from ‘package:dplyr’:
#>
#> collapse, desc, slice
#> The following objects are masked from ‘package:tidysq’:
#>
#> collapse, reverse
#> Loading required package: XVector
#> Loading required package: GenomeInfoDb
#>
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:ape’:
#>
#> complement
#> The following objects are masked from ‘package:tidysq’:
#>
#> alphabet, complement, translate
#> The following object is masked from ‘package:base’:
#>
#> strsplit
Biostrings_ami <- AAStringSet(c(one = "FEAPQLIWY", two = "EGITENAK"))
import_sq(Biostrings_ami)
#> # A tibble: 2 × 2
#> name sq
#> <chr> <ami_ext>
#> 1 one FEAPQLIWY <9>
#> 2 two EGITENAK <8>
# seqinr example
library(seqinr)
#>
#> Attaching package: ‘seqinr’
#> The following object is masked from ‘package:Biostrings’:
#>
#> translate
#> The following objects are masked from ‘package:ape’:
#>
#> as.alignment, consensus
#> The following object is masked from ‘package:dplyr’:
#>
#> count
#> The following object is masked from ‘package:tidysq’:
#>
#> translate
seqinr_dna <- as.SeqFastadna(c("C", "T", "C", "A"), name = "one")
import_sq(seqinr_dna)
#> # A tibble: 1 × 2
#> name sq
#> <chr> <dna_bsc>
#> 1 one CTCA <4>