probeAnno-class {Ringo} | R Documentation

## Class "probeAnno"

### Description

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

### Objects from the Class

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

### Slots

`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

### Methods

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

### Note

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

### Author(s)

Joern Toedling toedling@ebi.ac.uk; Wolfgang Huber

### See Also

posToProbeAnno

### Examples

      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"])

[Package Ringo version 1.8.0 Index]