complementSeq {matchprobes} | R Documentation

## Complementary sequence.

### Description

Function to obtain the complementary sequence.

### Usage

    complementSeq(seq, start=1, stop=0)

### Arguments

`seq` | Character vector consisting of the letters A, C, G and T.
`start` | Numeric scalar: the sequence position at which to start complementing. If 1, start from the beginning.
`stop` | Numeric scalar: the sequence position at which to stop complementing. If 0, go until the end.

### Details

The complemented sequence for each element of the input is computed and returned. The complement is given by the mapping: A -> T, C -> G, G -> C, T -> A.

An important special case is `start=13`, `stop=13`: If `seq` is a vector of 25mer sequences on an Affymetrix GeneChip, `complementSeq(seq, start=13, stop=13)` calculates the so-called mismatch sequences..

The function deals only with sequences that represent DNA. These can consist only of the letters `A`, `C`, `T` or `G`. Upper, lower or mixed case is allowed and honored.

### Value

A character vector of the same length as `seq` is returned. Each component represents the transformed sequence for the input value.

### Author(s)

R. Gentleman, W. Huber

### See Also

`basecontent`, `link{reverseSeq}`

### Examples

     seq <- c("AAACT", "GGGTT")
     complementSeq(seq)

     seq <- c("CGACTGAGACCAAGACCTACAACAG", "CCCGCATCATCTTTCCTGTGCTCTT")
     complementSeq(seq, start=13, stop=13)

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