alignmentOne {enhancerHomologSearch} | R Documentation

## Get alignment scores

### Description

Do pairwise alignment for query enhancer to target genome

### Usage

    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)

[Package enhancerHomologSearch version 1.0.1 Index]