remap {Starr} | R Documentation

## 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 A remapping is recommended if the bpmap file was built on an outdated genome, or if sequences, that match the genome more than once should be excluded.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

### Author(s)

Benedikt Zacher zacher@lmb.uni-muenchen.de

### 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)

[Package Starr version 1.38.0 Index]