cnvSimInterval: Generate a simulated interval

In daynefiler/mcCNV: Call copy number variants from whole exome/whole genome sequencing data

Description

Generate a simulated interval

Usage

cnvSimInterval(
  n = 1e+05,
  seqnames = "simSeq",
  meanlog = -12.36,
  sdlog = 0.7393,
  seed = NULL
)

Arguments

n	integer of length 1, the number of intervals
seqnames	character of length 1, 'seqnames' for the simulated intervals
meanlog	numeric of length 1, passed to rlnorm to define distribution of interval capture probabilities
sdlog	numeric of length 1, passed to rlnorm to define distribution of interval capture probabilities
seed	integer, passed to set.seed()

Details

cnvSimInterval generates an interval object with randomly-generated capture probabilities required for cnvSimCounts(). Interval capture probabilities are drawn initially from a lognormal distribution, then normalized to a sum of 1. The capture probabilities are stored in 'captureProb.'

The default values for meanlog & sdlog were derived from multiplexed whole- exome capture of 16 human samples using the Agilent XT2 capture platform.

cnvSimInterval does not intend to make realistic exon sizes or spacing. All simulated intervals are 50 basepairs wide with start sites every 200 basepairs. The structure of the object is simple and users can easily create their own interval objects containing capture probabilities if greater complexity is desired.

Setting the 'seed' parameter allows for reproducible simulation studies.

See Also

cnvSimCounts cnvSimPool

daynefiler/mcCNV documentation built on Dec. 15, 2021, 3:58 a.m.