alignmentOne: Get alignment scores

In jianhong/enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer

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)

jianhong/enhancerHomologSearch documentation built on Nov. 4, 2024, 8:29 p.m.