matchingSites {BCRANK} | R Documentation |
This function reports all occurrences of a consensus sequence in a fasta file. It can be used to extract transcription factor binding sites predicted by BCRANK or other motif search methods.
matchingSites(fafile, motifSequence, revComp=TRUE, strip.desc=TRUE)
fafile |
a ranked fasta file containing DNA sequences. |
motifSequence |
a character vector in IUPAC coding representing a DNA sequence. |
revComp |
set to TRUE if the reverse complement also be matched. |
strip.desc |
An argument used by the function readFASTA() .
It specifies whether or not the ">" marking at the beginning of description lines should be removed. |
Returns a data frame with positions, strand and DNA sequence for the matching sites.
Adam Ameur, adam.ameur@lcb.uu.se
Ameur, A., Rada-Iglesias, A., Komorowski, J., Wadelius, C. Novel algorithm and ChIP-analysis identifies candidate functional SNPs. Submitted