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