| as.data.frame.profileCGH {GLAD} | R Documentation |
Convert a profileCGH object into a data.frame.
as.data.frame.profileCGH(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.
People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.
Philippe Hupé, glad@curie.fr
data(snijders)
### Creation of "profileCGH" object
profileCGH <- as.profileCGH(gm13330)
###########################################################
###
### glad function as described in Hupé 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)