as.profileCGH {GLAD} | R Documentation

## Create an object of class profileCGH

### Description

Create an object of class profileCGH.

### Usage

    as.profileCGH(object,...)
    ## S3 method for class 'data.frame'
    as.profileCGH(object, infaction=c("value","empty"),
    value=20, keepSmoothing=FALSE, ...)

### Arguments

`object` | A data.frame to be convert into profileCGH.
`infaction` | If "value" then the LogRatio with infinite values (-Inf, Inf) are replace by + or - `value` according to the sign. If "empty" then NAs are put instead.
`value` | replace Inf by `value` if `infaction` is "value".
`keepSmoothing` | if TRUE the smoothing value in object is kept
`...` | ...

### Details

The data.frame to be convert must at least contain the following fields: LogRatio, PosOrder, and Chromosome. If the field Chromosome is of mode character, it is automatically converted into a numeric vector (see `ChrNumeric`); a field ChromosomeChar contains the character labels. The data.frame to be converted into a profileCGH objet is split into two data.frame: profileValuesNA contains the rows for which there is at least a missing value for either LogRatio, PosOrder or Chromosome; profileValues contains the remaining rows.

### Value

`` | A list with the following attributes
`profileValues` | A data.frame
`profileValuesNA` | A data.frame

### Note

People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.

### Author(s)

Philippe HupÃ©, glad@curie.fr

### See Also

`as.data.frame.profileCGH`

### Examples

    data(snijders)

    ### Creation of "profileCGH" object
    profileCGH <- as.profileCGH(gm13330)

    attributes(profileCGH)

[Package GLAD version 2.46.0 Index]