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 An argument used by the function readFASTA(). It specifies whether or not the ">" marking at the beginning of description lines should be removed.

Value

Returns a data frame with positions, strand and DNA sequence for the matching sites.

Author(s)

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

References

Ameur, A., Rada-Iglesias, A., Komorowski, J., Wadelius, C. Novel algorithm and ChIP-analysis identifies candidate functional SNPs. Submitted

See Also

bcrank


[Package BCRANK version 1.4.1 Index]