sequenza (version 3.0.0)

types.matrix: Creates a matrix of type tags

Description

Type tags are a utensil to distinguish genomic positions by their copy number state, number A and B alleles and the number of mutated alleles. This function creates a matrix of all possible type tags, given the copy number of the normal sample and the range of possible copy numbers in the tumor sample.

Usage

baf.types.matrix(CNt.min, CNt.max, CNn = 2)
    mufreq.types.matrix(CNt.min, CNt.max, CNn = 2)

Arguments

CNt.min

minimum copy number in the tumor.

CNt.max

maximum copy number in the tumor.

CNn

copy number of the normal sample.

Value

baf.types.matrix returns a data.frame with the 3 columns:

CNn

number of alleles in the normal sample.

CNt

numbers of alleles in the tumor sample.

B

number of B alleles in the tumor sample.

mufreq.types.matrix returns a data.frame with the 3 columns:

CNn

number of alleles in the normal sample.

CNt

numbers of alleles in the tumor sample.

Mt

number of mutated alleles in the tumor sample.

Details

A type consists of 3 integers signifying the copy number in the normal and tumor samples and the number of B alleles (baf.types.matrix) or mutated alleles (mufreq.types.matrix). The two functions return all the possible types combination within the range of tumor copy numbers in the arguments (CNt.min:CNt.max).

See Also

theoretical_mufreq, theoretical_depth_ratio, theoretical_baf, model_points.

Examples

# NOT RUN {
    ## Generate matrix types from 0 to 4 copy number, being the
    ## non-tumor chromosome diploid.
    baf.types.matrix(CNt.min = 0, CNt.max = 4, CNn = 2 )

    ## Generate matrix types from 0 to 4 copy number, being the
    ## non-tumor chromosome monoploid.
    mufreq.types.matrix(CNt.min = 0, CNt.max = 4, CNn = 1 )
# }