segmentData: Joint segmentation

In pneuvial/c3co: Cancer Cell Clonality using Copy-Number

Description

Joint segmentation by Recursive Binary Segmentation followed by Dynamic Programming

Usage

segmentData(dat, stat = c("C1C2", "TCN"), verbose = FALSE)

Arguments

dat	A list of data frames containing columns: tcn Total copy number dh Mirrored B allele fraction pos Position on the genome chr Chromosome
stat	"TCN" or "C1C2" parameter to segment the data. If stat == "TCN"', the segmentation will be done on TCN only.
verbose	A logical value indicating whether to print extra information. Defaults to FALSE.

Details

This function is a wrapper around the jointseg::jointSeg() of the jointseg package.

Value

Binned minor and major copy numbers with list of breakpoints.

References

Gey, S., & Lebarbier, E. (2008). Using CART to Detect Multiple Change Points in the Mean for Large Sample. http://hal.archives-ouvertes.fr/hal-00327146/

Pierre-Jean, M., Rigaill, G. & Neuvial, P. (2015). Performance evaluation of DNA copy number segmentation methods. Briefings in Bioinformatics 16 (4): 600-615

Examples

dataAnnotTP <- acnr::loadCnRegionData(dataSet="GSE11976", tumorFrac=1)
dataAnnotN <- acnr::loadCnRegionData(dataSet="GSE11976", tumorFrac=0)
len <- 500*10   ## Number of loci
K <- 3L         ## Number of subclones
n <- 15L        ## Number of samples
bkps <- list(c(100, 250)*10, c(150, 400)*10, c(150, 400)*10)
regions <- list(c("(0,3)", "(0,2)", "(1,2)"),
c("(1,1)", "(0,1)", "(1,1)"), c("(0,2)", "(0,1)", "(1,1)"))
datSubClone <- buildSubclones(len=len, nbClones=K, bkps=bkps, regions=regions,
                               dataAnnotTP=dataAnnotTP, dataAnnotN=dataAnnotN)
W <- rSparseWeightMatrix(nb.samp=n, nb.arch=K, sparse.coeff=0.7)
dat <- mixSubclones(subClones=datSubClone, W=W)
res <- segmentData(dat)
res2 <- segmentData(dat, stat="TCN")

pneuvial/c3co documentation built on May 25, 2019, 10:21 a.m.