bcrank {BCRANK} | R Documentation

## BCRANK: predicting binding site consensus from ranked DNA sequences

### Description

This function implements an algorithm for detection of short DNA sequences that are overrepresented in some part of the list. Starting from some initial consensus DNA sequence coded in IUPAC symbols, the method uses a heuristic search to improve the consensus until a local optimum is found. Individual predicted binding sites can be reported by the function `matchingSites`.

### Usage

    bcrank(fafile, startguesses=c(), restarts=10, length=10,
           reorderings=500, silent=FALSE, plot.progress=FALSE,
           do.search=TRUE, use.P1=FALSE, use.P2=TRUE, strip.desc=TRUE)

### Arguments

`fafile` | a ranked fasta file containing DNA sequences.
`startguesses` | a character vector with consensus sequences in IUPAC coding to be used as starting sequences in the search. If empty, random start guesses will be generated.
`restarts` | number restarts of the algorithm when using random start guesses.
`length` | legth of random start guess.
`reorderings` | number of random reorderings of the DNA sequences performed when calculating score.
`silent` | reports progress status if FALSE.
`plot.progress` | if TRUE, the progress is displayed in a plot.
`do.search` | if FALSE, no search is performed. In that case the start guesses are assigned with scores and reported as results.
`use.P1` | Use penalty for bases other than A,C,G,T.
`use.P2` | Use penalty for motifs matching repetitive sequences.
`strip.desc` | Ignored (always treated as TRUE).

### Value

The method returns an objcet of class `BCRANKresult-class`.

### 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

`matchingSites`, `BCRANKresult-class`

### Examples

    ## Load example fasta file
    fastaFile <- system.file("Exfiles/USF1_small.fa", package = "BCRANK")
    ## Run BCRANK
    ## Not run: BCRANKout <- bcrank(fastaFile, restarts=20)

    ## Show BCRANK results
    toptable(BCRANKout)
    ## The top scoring result
    topMotif <- toptable(BCRANKout,1)
    ## Plot BCRANK search path
    plot(topMotif)
    ## Position Weight Matrix
    pwm(topMotif, normalize=FALSE)

[Package BCRANK version 1.56.0 Index]