as.profileCGH: Create an object of class profileCGH

In GLAD: Gain and Loss Analysis of DNA

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 Hupé, [e-mail]

See Also

as.data.frame.profileCGH

Examples

data(snijders)

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

attributes(profileCGH)

GLAD documentation built on Nov. 8, 2020, 11:10 p.m.