Manipulate String Set

Orient and align DNA sequences in a DNA string set object.

Usage

ManipStringSet(DNAStringSet)

Arguments

DNAStringSet

A DNA string set object.

Value

A DNA string set (that is ready for analysis)

Examples

# generate and manipulate a DNA string set object using the taxon 'Antheraea polyphemus'

specdf_Anth <- querySpecData("Antheraea polyphemus")[1:10,]

DNABin_Anth <- genDNABin(specdf_Anth)

DNAStringset_Anth <- genDNAStringSet(DNABin_Anth)

DNAStringSet_Anth_manipulated <- ManipStringSet(DNAStringset_Anth)
#> ========================================================================================================================================================================================================
#> 
#> Time difference of 0.02 secs
#> Determining distance matrix based on shared 9-mers:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Clustering into groups by similarity:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Aligning Sequences:
#> ================================================================================
#> 
#> Time difference of 0.05 secs
#> 
#> Iteration 1 of 2:
#> 
#> Determining distance matrix based on alignment:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Reclustering into groups by similarity:
#> ================================================================================
#> 
#> Time difference of 0 secs
#> 
#> Realigning Sequences:
#> ================================================================================
#> 
#> Time difference of 0.05 secs
#> 
#> Alignment converged - skipping remaining iteration.
#>