remap {Starr} | R Documentation |
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 A remapping is recommended if the bpmap file was built on an outdated genome, or if sequences, that match the genome more than once should be excluded.
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)