| extractProbeAnno {Ringo} | R Documentation |
This function can be used to build a probeAnno object from the
reporter match positions given in the 'genes' slot of an RGList if
present, as is the case with some ChIP-chip microarray platforms,
e.g. with certain Agilent ones after reading in the data with
read.maimages(...,"agilent").
extractProbeAnno(object, format = "agilent", ...)
object |
an object that holds the data and the probe match
positions, currently can only be of class RGList |
format |
in which format are the reporter match positions stored in the object; see details; currently only "agilent" is implemented |
... |
further arguments that are passed on to the function
posToProbeAnno |
Which information is used for creating the probeAnno is specified by
the argument format.
RGList. The 'genes'
element of the object is taken. This element is expected to have
at least a column 'ProbeName', which stores the unique
reporter/probe identifiers, and a column 'SystematicName', which
holds the probe match position in the format
"chr<chromosome>:coordinate1-coordinate2",
e.g."chr1:087354051-087354110".
An object of class probeAnno holding the mapping between
reporters and genomic positions.
Joern Toedling toedling@ebi.ac.uk
posToProbeAnno, probeAnno-class