Helper function which cbind a list of XStringSet
into XStringSet
.
cbind_XStringSetList(x, type = "DNAStringSet")
list of XStringSet
type of XStringSet
[default: DNAStringSet]
name
##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...