peaks.fsa: Get maximal value in ranges
In MLPA: Multiplex Ligation-Dependent Probe Amplification Data Analysis

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	peaks.fsa(x, ranges, logTransform = FALSE, lowThreshold = 1000, channels = "6-FAM", noiseRange = c(-10, 0), primerRange = c(35, 45))

`x`	An aligned object of class `fsa`, as returned by `align.fsa`.
`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 `x` channel to browse.
`noiseRange`	Numeric vector of length 2, defining the range (relative to the starting range of the first peak defined in `ranges`) in which measure the noise (in bp). If the noise peak is 20 percent greater than the first peak, a warning is raised as the accuracy of the measure may be compromised.
`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 `ranges`.
`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

GEP.process

  # 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))