buildSubclones: Build (pure) subclones by resampling real copy-number data

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

Description

Build (pure) subclones by resampling real copy-number data

Usage

buildSubclones(len, nbClones, bkps, regions, dataAnnotTP = NULL,
  dataAnnotN = NULL, eps = 0.25)

Arguments

len	The number of loci in each subclone.
nbClones	The number of subclones.
bkps	A list of vectors of breakpoint positions for each subclone.
regions	A list of altered regions for each subclone.
dataAnnotTP	A data frame containing tumor data from which the subclone data are sampled, with columns: c total copy number b B allele fraction region type of DNA copy number alteration genotype germline genotype If NULL (default), this data frame is simulated using a simple model with Gaussian errors (on the scale of log-copy-numbers).
dataAnnotN	A data frame containing paired normal data from which the subclone data are sampled. Same format as argument dataAnnotTP. Must not be NULL if argument dataAnnotTP is not NULL.
eps	A numeric value, the signal to noise ratio for simulated data.

Details

The subclones are designed to mimic intra-tumor heterogeneity. In particular, all of the subclones generated by a single call to this function share the same germline genotypes. Their relative frequency corresponds to that of the input data.

If dataAnnotTP is provided, then the output data are simply sampled from it. Else, they are simulated as follows: (i) generate genotypes and minor and major copy number profiles, (ii) transform them back into more classical copy number estimates: total copy number and allele B fractions, ie the format described above for argument dataAnnotTP.

Value

A list of locus-level data sets for each subclone. Each data set is of the format described above for argument dataAnnotTP.

Examples

len <- 500*10  ## Number of loci
K <- 2L        ## Number of subclones
bkps <- list(c(100, 250)*10, c(150, 400)*10)
regions <- list(c("(0,1)", "(0,2)", "(1,2)"), c("(1,1)", "(0,1)", "(1,1)"))

## Resampling read copy number data
dataAnnotTP <- acnr::loadCnRegionData(dataSet="GSE13372", tumorFraction=1)
dataAnnotN <- acnr::loadCnRegionData(dataSet="GSE13372", tumorFraction=0)

datR <- buildSubclones(len=len, nbClones=K, bkps=bkps, regions=regions,
                       dataAnnotTP=dataAnnotTP, dataAnnotN=dataAnnotN)

## Simulated data
datS <- buildSubclones(len=len, nbClones=K, bkps=bkps, regions=regions)

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