xy2indices {affy} | R Documentation

## Functions to convert indices to x/y (and reverse)

### Description

Functions to convert indices to x/y (and reverse)

### Usage

    xy2indices(x, y, nr = NULL, cel = NULL, abatch = NULL, cdf = NULL, xy.offset = NULL)
    indices2xy(i, nr = NULL, cel = NULL, abatch = NULL, cdf = NULL, xy.offset = NULL)

### Arguments

`x` | `X` position for the probes
`y` | `Y` position for the probes
`i` | indices in the `AffyBatch` for the probes
`nr` | total number of `Xs` on the chip
`cel` | a corresponding object of class `Cel`
`abatch` | a corresponding object of class `AffyBatch`
`cdf` | character - the name of the corresponding cdf package
`xy.offset` | an eventual offset for the XY coordinates. See Details

### Details

The probes intensities for given probe set ids are extracted from an `AffyBatch` object using the indices stored in the corresponding `cdfenv`.

The parameter `xy.offset` is there for compatibility. For historical reasons, the xy-coordinates for the features on Affymetrix chips were decided to start at 1 (one) rather than 0 (zero). One can set the offset to 1 or to 0. Unless the you _really_ know what you are doing, it is advisable to let it at the default value `NULL`. This way the package-wide option code{xy.offset} is always used.

### Value

A vector of indices or a two-columns matrix of Xs and Ys.

### Warning

Even if one really knows what is going on, playing with the parameter `xy.offset` could be risky. Changing the package-wide option `xy.offset` appears much more sane.

### Author(s)

L.

### See Also

`indexProbes`

### Examples

    data(affybatch.example)

    pm.i <- indexProbes(affybatch.example, which="pm", genenames="AFFX-BioC-5_at")[[1]]
    mm.i <- indexProbes(affybatch.example, which="mm", genenames="AFFX-BioC-5_at")[[1]]

    pm.i.xy <- indices2xy(pm.i, abatch = affybatch.example)
    mm.i.xy <- indices2xy(mm.i, abatch = affybatch.example)

    image(affybatch.example[1], transfo=log2)
    ## plot the pm in red
    plotLocation(pm.i.xy, col="red")
    plotLocation(mm.i.xy, col="blue")

[Package affy version 1.14.2 Index]