searchSeq {TFBSTools} | R Documentation

## searchSeq method

### Description

It scans a nucleotide sequence with the pattern represented by a PWMatrix and identifies putative transcription factor binding sites.

### Usage

      searchSeq(x, subject, seqname="Unknown", strand="*", min.score="80%",
                mc.cores=1L)

### Arguments

`x` | `PWMatrix` or `PWMatrixList` object.
`subject` | A `DNAStringSet`, `DNAString`, `XStringViews` or `MaskedDNAString` object that will be scanned.
`seqname` | This is sequence name of the target sequence. If subject is a `DNAStringSet`, the names of the `DNAStringSet` object will be used.
`strand` | When searching the sequence, we can search the positive strand or negative strand. While strand is "*", it will search both strands and return the results based on the positvie strand coordinate.
`min.score` | The minimum score for the hit. Can be given an character string in the format of "80%" or as a single absolute value between 0 and 1. When it is percentage value, it represents the quantile between the minimal and the maximal possible value from the PWM.
`mc.cores` | `integer`(1): The number of cores to use. It is only used when ‘x’ is a `PWMatrixList` object and not available on windows platform.

### Value

A `SiteSet` object is returned when x is a `PWMatrix` object. A `SiteSetList` object is returned when x is a `PWMatrixList` or subject is a `DNAStringSet`.

### Author(s)

Ge Tan

### References

Wasserman, W. W., & Sandelin, A. (2004). Applied bioinformatics for the identification of regulatory elements. Nature Publishing Group, 5(4), 276-287. doi:10.1038/nrg1315

### See Also

`searchAln`, matchPWM

### Examples

      data(MA0003.2)
      data(MA0004.1)
      pwm1 <- toPWM(MA0003.2)
      pwm2 <- toPWM(MA0004.1)
      pwmList <- PWMatrixList(pwm1=pwm1, pwm2=pwm2)
      seq1 <- "GAATTCTCTCTTGTTGTAGCATTGCCTCAGGGCACACGTGCAAAATG"
      seq2 <- "GTTTCACCATTGCCTCAGGGCATAAATATATAAAAAAATATAATTTTCATC"

      # PWMatrix, character
      ## Only scan the positive strand of the input sequence
      siteset <- searchSeq(pwm1, seq1, seqname="seq1", strand="+", min.score="80%")
      siteset <- searchSeq(pwm1, seq1, seqname="seq1", strand="+", min.score=0.8)
      ## Only scan the negative strand of the input sequence
      siteset <- searchSeq(pwm1, seq1, seqname="seq1", strand="-", min.score="80%")
      ## Scan both strands of the input sequences
      siteset <- searchSeq(pwm1, seq1, seqname="seq1", strand="*", min.score="80%")
      ## Convert the SiteSet object into other R objects
      as(siteset, "data.frame")
      as(siteset, "DataFrame")
      as(siteset, "GRanges")
      writeGFF3(siteset)
      writeGFF2(siteset)

      # PWMatrixList, character
      sitesetList <- searchSeq(pwmList, seq1, seqname="seq1", strand="*",
                               min.score="80%")
      sitesetList <- searchSeq(pwmList, seq1, seqname="seq1", strand="*",
                               min.score="80%", mc.cores=1L)

      ## Convert the SiteSteList object into other R objects
      as(sitesetList, "data.frame")
      as(sitesetList, "DataFrame")
      as(sitesetList, "GRanges")
      writeGFF3(sitesetList)
      writeGFF2(sitesetList)

      # PWMatrix, DNAStringSet
      library(Biostrings)
      seqs <- DNAStringSet(c(seq1=seq1, seq2=seq2))
      sitesetList <- searchSeq(pwm1, seqs, min.score="80%")

      # PWMatrixList, DNAStringSet
      sitesetList <- searchSeq(pwmList, seqs, min.score="80%")

[Package TFBSTools version 1.28.0 Index]