probeAnnoClass: Class "probeAnno"
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Objects from the Class Slots Methods Note Author(s) See Also Examples

A class that holds the mapping between reporters/probes on a microarray and their genomic match position(s) in a chosen genome.

Objects can be created by calls of the form new("probeAnno", map, arrayName, genome).

map:

Object of class "environment" This map consists of four vectors for each chromosome/strand, namely, say for chromosome 1:

1.start: genomic start coordinates of probe matches on chromosome 1
1.end: genomic start coordinates of probe matches on chromosome 1
1.index: identifier of probes matching at these coordinates
1.unique: vector of the same length as the three before; encoding how many matches the corresponding probe has in the given file or data.frame. An entry of '0' indicates that the probe matching at this position has only this one match.

arrayName:

Object of class "character", the name or identifier of the microarray design, e.g. 2005-06-17\_Ren\_MM5Tiling\_Set1

genome:

Object of class "character", which genome the reporters have been mapped to

arrayName: obtain the microarray platform name
arrayName<-: replace the microarray platform name
[: get elements from the map environment
[<-: assign elements to the map environment
chromosomeNames: obtain a character vector holding the names of the chromosomes for which the probeAnno objects holds a mapping.
get: get elements from the map environment
initialize: create mew probeAnno object
ls: list elements of the map environment
genome: obtain the description of the genome the reporters were mapped to
genome<-: replace the description of the genome the reporters were mapped to
as: signature(from="environment"); function to coerce old-style 'probeAnno' environments to new-style 'probeAnno' objects. Simply creates a new object with the old environment in its map slot

'probeAnno' objects used to be environments and still are used as such in package tilingArray

Joern Toedling; Wolfgang Huber

posToProbeAnno

  pa <- new("probeAnno")
  pa["X.start"] <- seq(5000,10000,by=1000)
  if (interactive()) show(pa)
  pa2 <- posToProbeAnno(file.path(system.file("exData",package="Ringo"),
                                  "MOD_2003-12-05_SUZ12_1in2.pos"))
  arrayName(pa2) <- "NimbleGen MOD_2003-12-05_SUZ12_1in2"
  genome(pa2) <- "H. sapiens (hg18)"
  show(pa2)
  head(pa2["9.start"])