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)