Class "probeAnno"

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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

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  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"])

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