Modify one or more sequences to include Insertions or Deletions
indelcator(x, indels, ...)
# S4 method for XString,GRanges
indelcator(x, indels, exons, alt_col = "ALT", ...)
# S4 method for DNAStringSet,GRanges
indelcator(x, indels, alt_col = "ALT", mc.cores = 1, verbose = TRUE, ...)
# S4 method for BSgenome,GRanges
indelcator(x, indels, alt_col = "ALT", mc.cores = 1, names, ...)Sequence of class XString
GRanges object with InDel locations and the alternate allele
Passed to parallel::mclapply
GRanges object containing exon structure for x
Column containing the alternate allele
Number of cores to use when calling parallel::mclapply internally
logical(1) Print all messages
passed to BSgenome::getSeq when x is a BSgenome object
A DNAStringSet or XString object (See Details)
This is a lower-level function relied on by both transmogrify() and
genomogrify().
Takes an Biostrings::XString or Biostrings::XStringSet object and modifies the sequence to incorporate InDels. The expected types of data determine the behaviour, with the following expectations describing how the function will incorporate data
| Input Data Type | Exons Required | Use Case | Returned |
| XString | Y | Modify a Reference Transcriptome | XString |
| DNAStringSet | N | Modify a Reference Genome | DNAStringSet |
| BSgenome | N | Modify a Reference Genome | DNAStringSet |
## Start with a DNAStringSet
library(GenomicRanges)
seq <- DNAStringSet(c(seq1 = "AATCTGCGC"))
## Define an Insertion
var <- GRanges("seq1:1")
var$ALT <- "AAA"
seq
#> DNAStringSet object of length 1:
#> width seq names
#> [1] 9 AATCTGCGC seq1
indelcator(seq, var)
#> Updating seq1; Original length: 9
#> ; Updated length: 11
#> DNAStringSet object of length 1:
#> width seq names
#> [1] 11 AAAATCTGCGC seq1
## To modify a single transcript
library(GenomicFeatures)
#> Loading required package: AnnotationDbi
#> Loading required package: Biobase
#> Welcome to Bioconductor
#>
#> Vignettes contain introductory material; view with
#> 'browseVignettes()'. To cite Bioconductor, see
#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
ex <- GRanges(c("seq1:1-3:+", "seq1:7-9:+"))
orig <- extractTranscriptSeqs(seq, GRangesList(tx1 = ex))[["tx1"]]
orig
#> 6-letter DNAString object
#> seq: AATCGC
indelcator(orig, var, exons = ex)
#> 8-letter DNAString object
#> seq: AAAATCGC