matchingSites: Report IUPAC consensus occurrences in a fasta file
Description
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.
Usage
matchingSites(fafile, motifSequence, revComp=TRUE, strip.desc=TRUE)
Arguments
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
Ignored (always treated as TRUE).
Value
Returns a data frame with positions, strand and DNA sequence for the
matching sites.
References
Ameur, A., Rada-Iglesias, A., Komorowski, J., Wadelius,
C. Identification of candidate regulatory SNPs by combination of
transcription factor binding site prediction, SNP genotyping and
haploChIP. Nucleic Acids Res, 2009, 37(12):e85.