R: Consensus and profiles for sequence alignments

consensus {seqinr} | R Documentation

## Consensus and profiles for sequence alignments

### Description

This function returns a consensus using variuous methods (see details) or a profile from a sequence alignment.

### Usage

    consensus(matali, method = c( "majority", "threshold", "IUPAC", "profile"),
      threshold = 0.60, warn.non.IUPAC = FALSE, type = c("DNA", "RNA"))
    con(matali, method = c( "majority", "threshold", "IUPAC", "profile"),
      threshold = 0.60, warn.non.IUPAC = FALSE, type = c("DNA", "RNA"))

### Arguments

`matali` | an object of class `alignment` as returned by `read.alignment`, or a matrix of characters.
`method` | select the method to use, see details.
`threshold` | for the `threshold` method, a numeric value beteen 0 and 1 indicating the minimum relative frequency for a character to be returned as the consensus character. If none, NA is returned.
`warn.non.IUPAC` | for the `IUPAC` method this argument is passed to `bma` with a default value set to FALSE to avoid warnings due to gap characters in the alignment.
`type` | for the `IUPAC` method this argument is passed to `bma`.

### Details

"majority"

  The character with the higher frequency is returned as the consensus character.

"threshold"

  As above but in addition the character relative frequency must be higher than the value controled by the `threshold` argument. If none, NA id returned.

"IUPAC"

  Make sense only for nucleic acid sequences (DNA or RNA). The consensus character is defined if possible by an IUPAC symbol by function `bma`. If this is not possible, when there is a gap character for instance, NA is returned.

"profile"

  With this method a matrix with the count of each possible character at each position is returned.

`con` is a short form for `consensus`.

### Value

Either a vector of single characters with possible NA or a matrix with the method `profile`.

### Author(s)

J.R. Lobry

### References

`citation("seqinr")`

### See Also

See `read.alignment` to import alignment from files.

### Examples

    #
    # Read 5 aligned DNA sequences at 42 sites:
    #
      phylip <- read.alignment(file = system.file("sequences/test.phylip",
        package = "seqinr"), format = "phylip")
    #
    # Show data in a matrix form:
    #
      (matali <- as.matrix(phylip))
    #
    # With the majority rule:
    #
      res <- consensus(phylip)
      stopifnot(c2s(res) == "aaaccctggccgttcagggtaaaccgtggccgggcagggtat")
    #
    # With a threshold:
    #
      res.thr <- consensus(phylip, method = "threshold")
      res.thr[is.na(res.thr)] <- "." # change NA into dots
    # stopifnot(c2s(res.thr) == "aa.c..t.gc.gtt..g..t.a.cc..ggccg.......ta.")
      stopifnot(c2s(res.thr) == "aa.cc.tggccgttcagggtaaacc.tggccgg.cagggtat")
    #
    # With an IUPAC summary:
    #
      res.iup <- consensus(phylip, method = "IUPAC")
      stopifnot(c2s(res.iup) == "amvsbnkkgcmkkkmmgsktrmrssndkgcmrkdmmvskyaw")
      # replace 3 and 4-fold symbols by dots:
      res.iup[match(res.iup, s2c("bdhvn"), nomatch = 0) > 0] <- "."
      stopifnot(c2s(res.iup) == "am.s..kkgcmkkkmmgsktrmrss..kgcmrk.mm.skyaw")
    #
    # With a profile method:
    #
      (res <- consensus(phylip, method = "profile"))
    #
    # Show the connection between the profile and some consensus:
    #
      bxc <- barplot(res, col = c("green", "blue", "orange", "white", "red"), border = NA,
      space = 0, las = 2, ylab = "Base count",
      main = "Profile of a DNA sequence alignment",
      xlab = "sequence position", xaxs = "i")

      text(x = bxc, y = par("usr")[4],lab = res.thr, pos = 3, xpd = NA)
      text(x = bxc, y = par("usr")[1],lab = res.iup, pos = 1, xpd = NA)

[Package seqinr version 3.4-5 Index]