peaks.fsa: Get maximal value in ranges
In FSAtools: Fragment Analysis and Capillary Sequencing Tool Kit

peaks.fsa

R Documentation

Get maximal value in ranges

Description

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

Usage

  peaks.fsa(x, peaks, names, size.min, size.max, channels, colors,
    logTransform = FALSE, lowThreshold = 1000, noiseRange = c(-10, 0))

Arguments

`x`	An aligned object of class `fsa`, as returned by `align.fsa`.
`peaks`	A `data.frame` with one row for each peak to consider. Can be provided instead of individual `names` (corresponding to `peaks` row names instead of a column), `size.min`, `size.max`, `channels` and `colors` argument vectors.
`names`	Character vector, the names to give to the peaks (duplicated values should be avoided). If `peaks` is provided, this vector will be used instead.
`size.min`	Numeric vector, the minimal size (in base pairs) to look for the corresponding peak. If `peaks` is provided, this vector will be used instead.
`size.max`	Numeric vector, the maximal size (in base pairs) to look for the corresponding peak. If `peaks` is provided, this vector will be used instead.
`channels`	Character vector, the name of the channel in `x` in which to look for the corresponding peak. If `peaks` is provided, this vector will be used instead.
`colors`	Vector defining the color to use in future plots to highlight the corresponding peak. If `peaks` is provided, this vector will be used instead.
`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.
`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.

Value

Returns x, with a new or updated peaks attribute, a data.frame with a row for each range :

`size.min`	User-provided argument.
`size.max`	User-provided argument.
`channels`	User-provided argument.
`colors`	User-provided argument.
`size`	Size at which the maximum was found, in base pairs.
`height`	Maximum found, in fluorescence units.
`offScale`	Is there any off-scale value in the range ?
`normalized`	Current peak's height divided by the mean of all peak heights.

A normalized vector attribute is also set, corresponding to the normalized column only.

Author(s)

Sylvain Mareschal

Examples

  # Example FSA file provided
  fsa <- read.fsa(system.file("extdata/fsa_GEP/A5918.fsa", package="FSAtools"))
  fsa <- align.fsa(fsa)
  
  # Single custom interval
  fsa <- peaks.fsa(
    fsa,
    names = "IRF4",
    size.min = 86.2,
    size.max = 87.5,
    channels = "6-FAM",
    colors = "blue"
  )
  print(attr(fsa, "peaks"))
  
  # Using a design file
  design <- designFile(system.file("extdata/design_GEP.conf", package="FSAtools"))
  fsa <- peaks.fsa(fsa, peaks=design$GLOBALS$PEAKS)
  print(attr(fsa, "peaks"))

FSAtools documentation built on Aug. 19, 2023, 1:06 a.m.