sequenza (version 1.0.5)

model.points: Generate mutation frequency and depth ratio model point at given cellularity and ploidy value.

Description

model.points combines theoretical.mufreq and theoretical.depth.ratio to model the theoretical mutation frequency and depth ratio based on given values of cellularity and ploidy.

Usage

model.points(cellularity = 0.5, ploidy = 2, types = cbind(CNn = 2, CNt = 2, Mt = 1),
             avg.depth.ratio = 1)

Arguments

cellularity

fraction of tumor cells in the sample.

ploidy

2 * ratio between total DNA content in a tumor cell and a normal cell.

types

matrix with the sets of copy numbers and number of mutated alleles over which to model mutation frequency and depth ratio. The matrix can be generated with types.matrix.

avg.depth.ratio

average normalized depth ratio.

Value

• A matrix of two columns:
• mufreqs
  modelled values of mutation frequency for the given types.
• depth.ratio
  modelled values of depth ratio for the given types.

Details

model.points generates the theoretical values of mutation frequency and depth ratio for the given type tags. To learn more about type tags see types.matrix.

See Also

types.matrix, theoretical.depth.ratio, theoretical.mufreq.

Examples

# Simulate a cellularity of 0.5, ploidy of 2 and types from min CNt 0
# and max = 4 on an originally diploid genome:
types <- types.matrix(CNt.min = 0, CNt.max = 4, CNn = 2)
cbind(types, model.points(cellularity = 0.5, ploidy = 2,
                          types = types, avg.depth.ratio = 1))
# Simulate a cellularity of 0.5, ploidy of 2 and types from min CNt 0
# and max = 4 on an originally monoallelic genome:
types <- types.matrix(CNt.min = 0, CNt.max = 4, CNn = 1)
cbind(types, model.points(cellularity = 0.5, ploidy = 2,
                          types = types, avg.depth.ratio = 1))