extractProbeAnno: Build probeAnno from match positions in an RGList

In Ringo: R Investigation of ChIP-chip Oligoarrays

Description

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").

Usage

extractProbeAnno(object, format = "agilent", ...)

Arguments

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

Details

Which information is used for creating the probeAnno is specified by the argument format.

agilent

expects that the object is of class 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".

Value

An object of class probeAnno holding the mapping between reporters and genomic positions.

Author(s)

Joern Toedling

See Also

posToProbeAnno, probeAnno-class

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.