xy2indices {affy} | R Documentation |
Functions to convert indices to x/y (and reverse)
xy2indices(x, y, nr = NULL, cel = NULL, abatch = NULL, cdf = NULL, xy.offset = NULL) indices2xy(i, nr = NULL, cel = NULL, abatch = NULL, cdf = NULL, xy.offset = NULL)
x |
|
y |
|
i |
indices in the |
nr |
total number of |
cel |
a corresponding object of class |
abatch |
a corresponding object of class
|
cdf |
character - the name of the corresponding cdf package. |
xy.offset |
an eventual offset for the XY coordinates. See Details. |
The probes intensities for given probe set ids are extracted from an
AffyBatch
object using the indices stored in the corresponding
cdfenv
.
The parameter xy.offset
is there for compatibility.
For historical reasons, the xy-coordinates for the features
on Affymetrix chips were decided to start at 1 (one) rather than 0
(zero). One can set the offset to 1 or to 0. Unless the you \_really\_
know what you are doing, it is advisable to let it at the default
value NULL
. This way the package-wide option xy.offset
is
always used.
A vector of indices or a two-columns matrix of Xs and Ys.
Even if one really knows what is going on, playing with
the parameter xy.offset
could be risky. Changing the package-wide
option xy.offset
appears much more sane.
L.
if (require(affydata)) { data(Dilution) pm.i <- indexProbes(Dilution, which="pm", genenames="AFFX-BioC-5_at")[[1]] mm.i <- indexProbes(Dilution, which="mm", genenames="AFFX-BioC-5_at")[[1]] pm.i.xy <- indices2xy(pm.i, abatch = Dilution) mm.i.xy <- indices2xy(mm.i, abatch = Dilution) image(Dilution[1], transfo=log2) ## plot the pm in red plotLocation(pm.i.xy, col="red") plotLocation(mm.i.xy, col="blue") }