getxy.probeseq {altcdfenvs} | R Documentation |
A function to get the XY coordinates from a probes sequences data.frame
getxy.probeseq(ppset.id = NULL, probeseq = NULL, i.row = NULL, xy.offset = NULL, x.colname = "x", y.colname = "y")
ppset.id |
The probe sets of interest (a vector of mode character . |
probeseq |
The probe sequence data.frame (see details). |
i.row |
Row indexes in the data.frame (see details). |
xy.offset |
Offset for the xy coordinates. if NULL , uses
the default offset stored as an option for the affy package. |
x.colname, y.colname |
The probe sequence packages have seen the
names for the columns in their data.frame . This parameters
exists to let us follow these changes. |
The data.frame
passed as argument probeseq
is expected
to have (at least) the following columns: Probe.X
,
Probe.Y
and Probe.Set.Name
. When the argument
ppset.id
is not null, the probe sets
A matrix
of two columns. The first column contains x coordinates,
while the second column contains y coordinates.
The parameter xy.offset.one
is here for historical
reasons. This should not be touched, the option in the affy
package should be modified if one wishes to modify this.
This function should not be confused with the methods index2xy
and similar. Here the the XY coordinate come from a data.frame
that stores information about an arbitrary number probes on the
chip. (See the `probe sequence' data packages on Bioconductor, and the
package matchprobes
).
The methods index2xy
are meant to interact with instances of
class AffyBatch
.
Laurent
##---- Should be DIRECTLY executable !! ----