alignmentOne {enhancerHomologSearch} | R Documentation |
Do pairwise alignment for query enhancer to target genome
alignmentOne(query, subject, block = 1000, bpparam = bpparam(), ...)
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. |
An object of Enhancers.
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)