removeIndex: A function to remove probes in an environment
In altcdfenvs: alternative CDF environments (aka probeset mappings)

Description Usage Arguments Details Value Author(s) See Also Examples

A function to remove probes in an environment, given their index.

1	removeIndex(x, i, simplify = TRUE, verbose = FALSE)

`x`	An instance of `CdfEnvAffy-class`
`i`	A vector of indexes (integers !).
`simplify`	Simply the resulting `CdfEnvAffy` (see details).
`verbose`	verbose output or not.

The probes to be removed are set to NA in the CdfEnvAffy. When simplify is set to TRUE the probe sets are simplified whenever possible. For example, if both pm and mm for the same probe pair are set to NA, then the probe pair is removed from the probe set.

An instance of CdfEnvAffy-class is returned.

Laurent Gautier

CdfEnvAffy-class

## use plasmodiumanopheles chip as an example
if (require(plasmodiumanophelescdf)) {

  ## wrap in a (convenient) CdfEnvAffy object
  planocdf <- wrapCdfEnvAffy(plasmodiumanophelescdf, 712, 712, "plasmodiumanophelescdf")
  print(planocdf)

  ## ask for the probe indexed '10759' to be removed
  ## (note: if one wishes to remove from X/Y coordinates,
  ## the function xy2index can be of help).
  planocdfCustom <- removeIndex(planocdf, as.integer(10759))

  ## let see what happened (we made this example knowing in which
  ## probe set the probe indexed '10759' is found).
  indexProbes(planocdf, "pm", "200000_s_at")
  indexProbes(planocdfCustom, "pm", "200000_s_at")
  ## The 'second' pm probe (indexed '10579') in the probe set is now set
  ## to NA.
}