Get alignment scores

Do pairwise alignment for query enhancer to target genome

alignmentOne(query, subject, block = 1000, bpparam = bpparam(), ...)

Arguments

query

An object of DNAStringSet to represent enhancer

subject

Output of getENCODEdata. An object of Enhancers

block

The size of sequences to do alignment. Increase the size will increase the memory cost. Default 1000.

bpparam

BiocParallel parameters.

...

not used.

Value

An object of Enhancers.

Examples

library(BiocParallel)
bpparam <- MulticoreParam(workers = 1, tasks=200, progressbar=TRUE)
library(BSgenome.Hsapiens.UCSC.hg38)
peaks <- GRanges("chr1", IRanges(seq(5000, 50000, by=1000), width=1000))
peaks$id <- paste(seq_along(peaks), 1, sep="_")
subj <- Enhancers(genome=Hsapiens, peaks=peaks)
q <- getSeq(Hsapiens, GRanges("chr1", IRanges(90000, width=1000)))
ao <- alignmentOne(q, subj, bpparam=bpparam)
#> 
  |                                                                            
  |                                                                      |   0%
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  |======================================================================| 100%
#>