sequenza (version 1.0.5)

types.matrix: Creates a dataframe of type tags

Description

Type tags are a utensil to distinguish genomic positions by their copy number state and the number of mutated alleles. This function creates a dataframe 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

types.matrix(CNt.min = 1, CNt.max = 7, 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

• types.matrix returns a dataframe with the following columns:
• CNn
  number of alleles in the normal sample.
• CNt
  numbers of alleles in the aberrant sample
• Mt
  number of mutated alleles

Details

A type tag consists of 3 integers signifying the copy number in the normal and tumor samples and the number of mutated alleles. types.matrix returns all the possible type tags that can be created within the given range of tumor copy numbers.

See Also

theoretical.mufreq, theoretical.depth.ratio, theoretical.baf, model.points.

Examples

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