MLPA (version 1.10.0)

peaks.fsa: Get maximal value in ranges

Description

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

Usage

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

Arguments

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.

Value

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.

See Also

GEP.process

Examples

# NOT RUN {
  # 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))
# }