as.data.frame.profileCGH: profileCGH consercion
In GLAD: Gain and Loss Analysis of DNA

Description Usage Arguments Details Value Note Author(s) See Also Examples

Convert a profileCGH object into a data.frame.

1 2	## S3 method for class 'profileCGH' as.data.frame(x, row.names = NULL, optional = FALSE, ...)

`x`	The object to converted into data.frame.
`row.names`	NULL or a character vector giving the row names for the data frame. Missing values are not allowed.
`optional`	logical. If 'TRUE', setting row names and converting column names (to syntactic names) is optional.
`...`	...

The attributes profileValues and profileValuesNA are binded into a data.frame.

A data.frame object

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

Philippe HupÃ©, glad@curie.fr

as.profileCGH

data(snijders)

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



###########################################################
###
###  glad function as described in HupÃ© et al. (2004)
###
###########################################################


res <- glad(profileCGH, mediancenter=FALSE,
                smoothfunc="lawsglad", bandwidth=10, round=2,
                model="Gaussian", lkern="Exponential", qlambda=0.999,
                base=FALSE,
                lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,
                type="tricubic", param=c(d=6),
                alpha=0.001, msize=5,
                method="centroid", nmax=8,
                verbose=FALSE)


res <- as.data.frame(res)