peakAdjust: Translate and Scale Linear Data
In ornelles/flowExtra: Helper Functions for flowCore

Description Usage Arguments Details Value Examples

View source: R/peakAdjust.R

Scale linear DNA content to have identical "G1" peak values

peakAdjust(
  fs,
  chan = "FL2.A",
  peaks,
  g1 = 200,
  ratio = 1.92,
  limits = NULL,
  ...
)

`fs`	A `flowSet` with data to be transformed in channel in `chan`
`chan`	Character vector to specify the channel to normalize (`"FL2.A"`)
`peaks`	An optional matrix of "G1" and "G2/M" peak values or a vector of "G1" values. If missing, `peakFind()` to identify the peaks within the range specified by `range.search`
`g1`	Value of the rescaled G1 peak (`200`)
`ratio`	G2 to G1 ratio to place missing peaks "G1" peaks given a corresponding "G2/M" peak, default value of `1.90`
`limits`	Optional numeric vector of length 2 specifying the limits for the transformed data. If `NULL`, the instrument range for data in `chan` will be used. If `FALSE` the range will be `-Inf` to `+Inf`.
`...`	Optional arguments passed to `peakFind()` and then to `flowStats::curv1Filter()` including `range.search`, `probs`, `bwFac` and `gridsize`
`range.search`	A numeric vector of length 2 specifying the range of values in the original data in which peaks will be accepted. The default value of `c(50, 500)` is chosen to ignore apoptotic values and polyploid peaks in typical data

This function scales linear DNA content in chan to align peaks corresponding to a "G1" population of cells. Data will be adjusted by scaling the values in each flowFrame to place the "G1" peak at the value in g1.

The position of the actual "G1" population (and "G2/M" population) is provided in the optional argument peaks. This can either be a vector of "G1" peak positions or a matrix of "G1" and "G2/M" peak positions. A larger matrix will be accepted, such as one produced with peakFind(), but only the first two columns will be used and treated as "G1" and "G2/M" positions, respectively. Missing values in "G1" that have a "G2/M" value will be replaced by a value derived from ratio. If the argument peaks is missing, the function peakFind() will be called with arguments range.search and ... to identify the peaks.

Transformed values will be trimmed to the range specified by limits or the instrument range for chan if limits = NULL. No trimming will occur if limits = FALSE.

A transformed and scaled flowSet.

 fs <- readSet(system.file("extdata", "synch/", package = "flowExtra"))
 bf <- boundaryFilter("FL2.A")
 lg <- linearGate(fs)
 fs <- Subset(fs, bf & lg)
 o1 <- dnaplot(~FL2.A, fs, xlim = c(120, 380), main = "Raw", plot = FALSE)
 pks <- peakFind(fs, range.search = c(100, 400))
 fs.adj <- peakAdjust(fs, peaks = pks, g1 = 180)
 o2 <- dnaplot(~FL2.A, fs.adj, xlim = c(120, 380), main = "Adjusted", plot = FALSE)
 plot(o1, split = c(1, 1, 2, 1), more = TRUE)
 plot(o2, split = c(2, 1, 2, 1), more = FALSE)