type_matrix: Creates a matrix of type tags

In sequenza: Copy Number Estimation from Tumor Genome Sequencing Data

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.

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).

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.

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.
    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 )

Example output

  CNn CNt B
1   2   0 0
2   2   1 0
3   2   2 0
4   2   2 1
5   2   3 0
6   2   3 1
7   2   4 0
8   2   4 1
9   2   4 2
   CNn CNt Mt
1    1   0  0
2    1   1  0
3    1   1  1
4    1   2  0
5    1   2  1
6    1   2  2
7    1   3  0
8    1   3  1
9    1   3  2
10   1   3  3
11   1   4  0
12   1   4  1
13   1   4  2
14   1   4  3
15   1   4  4

sequenza documentation built on May 9, 2019, 5:04 p.m.