Description Usage Arguments Value Author(s) See Also Examples

Look for the maximal value in one or many ranges, typically for peak detection.

1 2 |

`x` |
An aligned object of class |

`ranges` |
A named list of ranges, numeric vectors of length two (minimal and maximal values). They defines the sizes (in base pairs) for which a maximum is required. |

`logTransform` |
Single logical value, whether to apply log transformation (base 2) to normalized values (previously floored to 0 and summed with 1) or not. |

`lowThreshold` |
Single numeric value, threshold for which "low profile" warnings are called if all peaks are lower. |

`channels` |
Single character value, the name of the |

`noiseRange` |
Numeric vector of length 2, defining the range (relative to the starting range of the first peak defined in |

`primerRange` |
Numeric vector of length 2, defining the range in which measure primer signals (in bp). This is implemented for QC experimentation and may not be useful in current practice. |

Returns a `data.frame`

with a row for each range :

`gene` |
The name of the range described, extracted from |

`size.min` |
Minimal size of the range described. |

`size.max` |
Maximal size of the range described. |

`peak.size` |
Size at which the maximum was found, in base pairs. |

`peak.height` |
Maximum found, in fluorescence units. |

`peak.offScale` |
Is there any off-scale value in the range ? |

`normalized` |
Current peak's height divided by the mean of all peak heights. |

Sylvain Mareschal

1 2 3 4 5 6 7 8 9 10 | ```
# Example FSA file provided
fsa <- read.fsa(system.file("extdata/fsa/A5918.fsa", package="MLPA"))
fsa <- align.fsa(fsa)
# Single interval
print(peaks.fsa(fsa, ranges=list(IRF4=c(86.2, 87.5))))
# Using a design file
design <- designFile(system.file("extdata/design.conf", package="MLPA"))
print(peaks.fsa(fsa, ranges=design$PEAKS$ranges))
``` |

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