c3co: Cancer subclone inference

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

Description

Cancer subclone inference

Usage

c3co(dat, parameters.grid = NULL, stat = c("C1C2", "TCN"),
  segDat = NULL, ..., verbose = FALSE)

Arguments

dat	A list of data frames for each patient, each of them of the form: tcn Total copy number dh Mirrored B allele fraction pos Position on the genome chr Chromosome
parameters.grid	Is a list composed of : the penalty coefficients named either lambda, lambda1 and lambda2. For the model on minor and major CN, it is possible to give two grids (one for minor CN and one for major CN), and all combination is tested. If only one grid is given the consider that lambda1 = lambda2. and composed of : a vector named nb.arch of integers which is the number of features in the model.
stat	"TCN" or "C1C2".
segDat	Either a path to the file that contains segmentation (‘*.rds’ file), by default NULL, or a file that contains segmentation (e.g. from segmentData()).
...	Further arguments to be passed to fitC3co().
verbose	A logical value indicating whether to print extra information. Defaults to FALSE.

Value

An object of class c3coFit.

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
set.seed(88)
bkps <- list(c(100, 250)*10, c(150, 400)*10, c(150, 400)*10)
regions <- list(c("(1,2)", "(0,2)", "(1,2)"),
c("(0,3)", "(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)
l1 <- seq(from=1e-6, to=1e-4, length.out=10L)
parameters.grid <- list(lambda=l1, nb.arch=2:5)
res <- c3co(dat, parameters.grid=parameters.grid)
## FIXME: BUG: propagate NA when rank deficient
## FIXME: resC <- c3co(dat, stat="TCN", parameters.grid =parameters.grid)

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