segmentData {CGHcall} | R Documentation |
A wrapper function to run existing breakpoint detection algorithms on arrayCGH data. Currently only DNAcopy is implemented.
segmentData(input, method = "DNAcopy", ...)
input |
Object of class cghRaw . |
method |
The method to be used for breakpoint detection. Currently only 'DNAcopy' is supported, which will run the segment function. |
... |
Arguments for segment . |
See segment
for details on the algorithm.
This function returns a dataframe in the same format as the input with segmented arrayCGH data.
Sjoerd Vosse & Mark van de Wiel
Venkatraman, A.S., Olshen, A.B. (2007). A faster circulary binary segmentation algorithm for the analysis of array CGH data. Bioinformatics, 23, 657-663.
data(Wilting) ## Convert to this-is-escaped-codenormal-bracket27bracket-normal object cgh <- make_cghRaw(Wilting) ## First preprocess the data raw.data <- preprocess(cgh) ## Simple global median normalization for samples with 75% tumor cells perc.tumor <- rep(0.75, 3) normalized.data <- normalize(raw.data, cellularity=perc.tumor) ## Segmentation with slightly relaxed significance level to accept change-points. ## Note that segmentation can take a long time. ## Not run: segmented.data <- segmentData(normalized.data, alpha=0.02)