extractProbeAnno {Ringo} | R Documentation

## Build probeAnno from match positions in an RGList

### 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`

[Package Ringo version 1.58.0 Index]