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 still are used as such in package `tilingArray`

### Author(s)

Joern Toedling; 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 1.58.0 Index]