setFlag.MicroarrayData: Sets the flags on some of the spots

In HenrikBengtsson/aroma: An R Object-oriented Microarray Analysis package

Description

Sets the flags on some of the spots. See also *addFlag() which adds/removes flags to already set flags.

Usage

## S3 method for class 'MicroarrayData'
setFlag(this, flag, include=NULL, exclude=NULL, slide=NULL, include.op="and", exclude.op="or", ...)

Arguments

flag	The name of the flag.
include	The indices of the spots that should be included. If it is instead a name of one or more flags, the spots which have been flagged with these flags are considered. If NULL all spots are considered.
exclude	The indices of the spots that should be excluded. If it is instead a name of one or more flags, the spots which have been flagged with these flags are excluded. If NULL no spots are excluded.
slide	Slide(s) to be considered. If NULL all slides are considered.
include.op	If "and" a spot must be flagged by all the flags to be included, and if the value is "or" it enough if spot is flagged by only one of the flags. Note that this argument is only effective if the include argument(s) are flag names.
exclude.op	If "and" a spot must be flagged by all the flags to be excluded, and if the value is "or" it enough if spot is flagged by only one of the flags. Note that this argument is only effective if the exclude argument(s) are flag names.

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

See Also

*addFlag(), *getFlag(), *clearFlag(), *listFlags(), *getInclude(). For more information see MicroarrayData.

Examples

  SMA$loadData("mouse.data")
  layout <- Layout$read("MouseArray.Layout.dat", path=system.file("data-ex", package="aroma"))
  raw <- RawData(mouse.data, layout=layout)
  ma <- getSignal(raw)
  normalizeWithinSlide(ma, "s")
  tma <- as.TMAData(ma)
  setFlag(tma, "Top 5% M's", top(abs(tma$M), 0.05))
  setFlag(tma, "Top 5% T's", top(abs(tma$T), 0.05))
  setFlag(tma, "Top 5% M's AND top 5% T's", c("Top 5% M's", "Top 5% T's"))
  plot(tma)
  highlight(tma, "Top 5% M's", col="red")
  highlight(tma, "Top 5% T's", col="blue")
  highlight(tma, "Top 5% M's AND top 5% T's", col="purple")

HenrikBengtsson/aroma documentation built on May 7, 2019, 12:56 a.m.