mm {oligo} | R Documentation

## Accessors and replacement methods for the intensity/PM/MM/BG matrices.

### Description

Accessors and replacement methods for the PM/MM/BG matrices.

### Usage

    intensity(object)
    mm(object, subset = NULL, target='core')
    pm(object, subset = NULL, target='core')
    bg(object, subset = NULL)
    mm(object, subset = NULL, target='core')<-value
    pm(object, subset = NULL, target='core')<-value
    bg(object)<-value

### Arguments

`object` | `FeatureSet` object.
`subset` | Not implemented yet.
`value` | `matrix` object.
`target` | One of 'probeset', 'core', 'full', 'extended'. This is ignored if the array design is something other than Gene ST or Exon ST.

### Details

For all objects but `TilingFeatureSet`, these methods will return matrices. In case of `TilingFeatureSet` objects, the value is a 3-dimensional array (probes x samples x channels).

`intensity` will return the whole intensity matrix associated to the object. `pm`, `mm`, `bg` will return the respective PM/MM/BG matrix.

When applied to `ExonFeatureSet` or `GeneFeatureSet` objects, `pm` will return the PM matrix at the transcript level ('core' probes) by default. The user should set the `target` argument accordingly if something else is desired. The valid values are: 'probeset' (Exon and Gene arrays), 'core' (Exon and Gene arrays), 'full' (Exon arrays) and 'extended' (Exon arrays).

The `target` argument has no effects when used on designs other than Gene and Exon ST.

### Examples

    if (require(maqcExpression4plex) & require(pd.hg18.60mer.expr)){
    xysPath <- system.file("extdata", package="maqcExpression4plex")
    xysFiles <- list.xysfiles(xysPath, full.name=TRUE)
    ngsExpressionFeatureSet <- read.xysfiles(xysFiles)
    pm(ngsExpressionFeatureSet)[1:10,]
    }

[Package oligo version 1.48.0 Index]