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`

, `reverseSeq`

### Examples

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

[Package

*matchprobes* version 1.2.1

Index]