matchprobes {matchprobes} | R Documentation

## A function to match a query sequence to the sequences of a set of probes.

### Description

The `query` sequence, a character string (probably representing a transcript of interest), is scanned for the presence of exact matches to the sequences in the character vector `records`. The indices of the set of matches are returned.

### Usage

    matchprobes(query, records, probepos=FALSE)

### Arguments

`query` | A character vector. For example, each element may represent a gene (transcript) of interest.
`records` | A character vector. For example, each element may represent the probes on a DNA array.
`probepos` | A logical value. If TRUE, return also the start positions of the matches in the query sequence.

### Details

The matching is done using the C library function `strstr`. It might be nice to explore other possibilities.

### Value

A list. Its first element is a list of the same length as the input vector. Each element of the list is a numeric vector containing the indices of the probes that have a perfect match in the query sequence.
If `probepos` is TRUE, the returned list has a second element: it is of the same shape as described above, and gives the respective positions of the matches.

### Author(s)

R. Gentleman, Laurent Gautier, Wolfgang Huber

### Examples

      ## The main intention for this function is together with the probe
      ## tables from the "probe" data packages, e.g.:
      ## > library(hgu95av2probe)
      ## > data(probe)
      ## > seq <- probe$sequence
      ##
      ## Since we do not want to be dependent on the presence of this
      ## data package, for the sake of example we simply simulate some
      ## probe sequences:

      bases <- c("A", "C", "G", "T")
      seq   <- sapply(1:1000, function(x) paste(bases[ceiling(4*runif(256))], collapse=""))

      w1 <- seq[20:22]
      w2 <- complementSeq(w1, start=13, stop=13)
      w  <- c(w1, w2)

      matchprobes(w, seq)
      matchprobes(w, seq, probepos=TRUE)

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