matchingSites: Report IUPAC consensus occurrences in a fasta file
In BCRANK: Predicting binding site consensus from ranked DNA sequences
Description
Usage
Arguments
Value
Author(s)
References
See Also
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
1
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 documentation built on Nov. 8, 2020, 8:21 p.m.
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Description Usage Arguments Value Author(s) References See Also
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
1 | 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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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