Starr (version 1.28.0)

remap: Remap reporter sequences to the genome and create a new bpmap file

Description

This function remaps the reporter sequences on the chip on the genome and outputs a new bpmap annotation, containing only unique matches to the genome. A remapping is recommended if the bpmap file was built on an outdated genome, or if sequences, that match the genome more than once should be excluded.

Usage

remap(bpmap=NULL, seqs=NULL, nseq=NULL, path="", complementary=FALSE, reverse=FALSE, reverse_complementary=FALSE, return_bpmap=FALSE)

Arguments

bpmap

A list, created by the function readBpmap() from the affy package.

nseq

Number of sequences, that are searched in one iteration.

seqs

Sequences to search as a character vector

path

path to genomic fasta files

complementary

If TRUE, the sequences are searched in the complementary strand of the text

reverse

If TRUE, the sequences are searched in the reverse strand of the text

reverse_complementary

If TRUE, the sequences are searched in the reverse complementary strand of the text

return_bpmap

If TRUE, the output is a list in bpmap format

Examples

# dataPath <- system.file("extdata", package="Starr")

# bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))
# newbpmap <- remap(bpmapChr1, nseq=5000000, path=dataPath, reverse_complementary=TRUE, return_bpmap=TRUE)