remap: Remap reporter sequences to the genome and create a new bpmap...
In Starr: Simple tiling array analysis of Affymetrix ChIP-chip data

Description Usage Arguments Author(s) Examples

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 A remapping is recommended if the bpmap file was built on an outdated genome, or if sequences, that match the genome more than once should be excluded.

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

`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

Benedikt Zacher zacher@lmb.uni-muenchen.de

# 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)

Starr documentation built on April 28, 2020, 7:52 p.m.