| xy2indices {affy} | R Documentation |
Functions to convert indices to x/y (and reverse)
xy2indices(x, y, nr = NULL, cel = NULL, abatch = NULL, xy.offset = NULL) indices2xy(i, nr = NULL, cel = NULL, abatch = NULL, xy.offset = NULL)
x |
X position for the probes |
y |
Y position for the probes |
i |
indices in the AffyBatch for the probes |
nr |
total number of Xs on the chip |
cel |
a corresponding object of class Cel |
abatch |
a corresponding object of class
AffyBatch |
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 code{xy.offset} is
always used.
A vector of indices or a two-columns matrix of Xs and Ys.
L.
data(affybatch.example) pm.i <- indexProbes(affybatch.example, which="pm", genenames="AFFX-BioC-5_at")[[1]] mm.i <- indexProbes(affybatch.example, which="mm", genenames="AFFX-BioC-5_at")[[1]] pm.i.xy <- indices2xy(pm.i, abatch = affybatch.example) mm.i.xy <- indices2xy(mm.i, abatch = affybatch.example) image(affybatch.example[1], transfo=log2) ## plot the pm in red plotLocation(pm.i.xy, col="red") plotLocation(mm.i.xy, col="blue")