Helper function which cbind a list of XStringSet into XStringSet.

cbind_XStringSetList(x, type = "DNAStringSet")

Arguments

x

list of XStringSet

type

type of XStringSet [default: DNAStringSet]

name

name

Author

Kristian K Ullrich

Examples

##load example sequence data
data("mousePRDM9", package="repeatR")
myRepPattern<-"PY"
myRepLength<-84
mousePRDM9.random<-sample(mousePRDM9, 4)
mousePRDM9.random.split<-repeatR::splitRepByPattern(mousePRDM9.random,
    myRepPattern, myRepLength)
repeatR::cbind_XStringSetList(mousePRDM9.random.split$cds,
    type="DNAStringSet")
#> $`AB844004.1_Mmd_Ttf/tw12+`
#> DNAStringSet object of length 1:
#>     width seq                                               names               
#> [1]   840 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG AB844004.1_Mmd_Tt...
#> 
#> $`AB844114.1_Mmmol_R209-wm7`
#> DNAStringSet object of length 1:
#>     width seq                                               names               
#> [1]   840 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG AB844114.1_Mmmol_...
#> 
#> $`AB843895.1_Mmd_RFM/J`
#> DNAStringSet object of length 1:
#>     width seq                                               names               
#> [1]  1008 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG AB843895.1_Mmd_RFM/J
#> 
#> $MK848144.1_cds_QCI31722.1_1
#> DNAStringSet object of length 1:
#>     width seq                                               names               
#> [1]  1176 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG MK848144.1_cds_QC...
#> 
repeatR::cbind_XStringSetList(mousePRDM9.random.split$aa,
    type="AAStringSet")
#> $`AB844004.1_Mmd_Ttf/tw12+`
#> AAStringSet object of length 1:
#>     width seq                                               names               
#> [1]   280 PYVCRECGRGFTAKSSLVQHQRT...ECGRGFTQKSDLIQHQRTHTREK AB844004.1_Mmd_Tt...
#> 
#> $`AB844114.1_Mmmol_R209-wm7`
#> AAStringSet object of length 1:
#>     width seq                                               names               
#> [1]   280 PYVCRECGRGFTAKSNLIQHQRT...ECGWGFTQKSDLIQHQRTHTREK AB844114.1_Mmmol_...
#> 
#> $`AB843895.1_Mmd_RFM/J`
#> AAStringSet object of length 1:
#>     width seq                                               names               
#> [1]   336 PYVCRECGRGFTQNSHLIQHQRT...ECGWGFTQKSDLIQHQRTHTREK AB843895.1_Mmd_RFM/J
#> 
#> $MK848144.1_cds_QCI31722.1_1
#> AAStringSet object of length 1:
#>     width seq                                               names               
#> [1]   392 PYVCRECGRGFTQNSHLIQHQRT...ECGWGFTQKSDLIQHQRTHTREK MK848144.1_cds_QC...
#> 
repeatR::collapse_XStringSetList(repeatR::cbind_XStringSetList(
    mousePRDM9.random.split$cds, type="DNAStringSet"))
#> DNAStringSet object of length 4:
#>     width seq                                               names               
#> [1]   840 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG AB844004.1_Mmd_Tt...
#> [2]   840 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG AB844114.1_Mmmol_...
#> [3]  1008 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG AB843895.1_Mmd_RFM/J
#> [4]  1176 CCCTATGTTTGCAGGGAGTGTGG...AGAGGACACATACAAGAGAGAAG MK848144.1_cds_QC...
repeatR::collapse_XStringSetList(repeatR::cbind_XStringSetList(
    mousePRDM9.random.split$aa, type="AAStringSet"))
#> AAStringSet object of length 4:
#>     width seq                                               names               
#> [1]   280 PYVCRECGRGFTAKSSLVQHQRT...ECGRGFTQKSDLIQHQRTHTREK AB844004.1_Mmd_Tt...
#> [2]   280 PYVCRECGRGFTAKSNLIQHQRT...ECGWGFTQKSDLIQHQRTHTREK AB844114.1_Mmmol_...
#> [3]   336 PYVCRECGRGFTQNSHLIQHQRT...ECGWGFTQKSDLIQHQRTHTREK AB843895.1_Mmd_RFM/J
#> [4]   392 PYVCRECGRGFTQNSHLIQHQRT...ECGWGFTQKSDLIQHQRTHTREK MK848144.1_cds_QC...