removeIndex {altcdfenvs} | R Documentation |
A function to remove probes in an environment, given their index.
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
## 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. }