matchingSites {BCRANK}R Documentation

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.

Author(s)

Adam Ameur, adam.ameur@genpat.uu.se

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.

See Also

bcrank


[Package BCRANK version 1.55.0 Index]