estimateSVSizes: Draw random structural variation sizes from a beta...

In Budheimer/RSVSim: RSVSim: an R/Bioconductor package for the simulation of structural variations

Description

RSVSim can implement structural variations (SVs) of specific sizes. estimateSVSizes draws random values for SV sizes from a beta distribution. It can fit the distribution according to given SV sizes or default values.

Usage

estimateSVSizes(n, svSizes, minSize, maxSize, default, hist=TRUE)

Arguments

n	The number of SVs to simulate
svSizes	A numeric vector with SV sizes to calculate the parameters for the beta distribution
minSize	The minimum returned SV size
maxSize	The maximum returned SV size
hist	TRUE or FALSE to show a histogram of the SV sizes (or not)
default	Setting this to "deletions", "insertions", "inversions" or "tandemDuplications" loads default shape parameters for the beta distribution for these SV types (see details below)

Details

• minSize and maxSize are optional and taken from the given set of svSizes if omitted

• The default shape parameters for deletions, insertions, inversions and tandem duplications were estimated from sequencing studies in the Database of Genomic Variants release 2012-03-29. In total, 1.129 deletions, 490 insertions, 202 inversions and 145 tandem duplications between 500bp and 10kb were used to estimate the shape of the distribution.

Value

A numeric vector with beta distributed values between minSize and maxSize.

Note

• It is intended to run this function separately for every SV type and then provide the output to the respective size argument of simulateSV

• It is recommended to use a minSize and maxSize that is consistent with the minimum/maximum values in svSizes.

• When using default shape parameters for the beta distribution, it works best to simulate SVs that do not differ too much in size (aroung 500bp-10kb).

Author(s)

Christoph Bartenhagen

References

Database of Genomic Variants: http://dgvbeta.tcag.ca/dgv/app/home?ref=NCBI36/hg18

Examples

  ## estimate sizes for 20 SVs from a given set of values:
  svSizes = c(10,20,30,40,60,80,100,150,200,250,300,400,500,750,1000)
  estimateSVSizes(n=20, svSizes=svSizes, hist=FALSE) 

  ## when using the default shape parameters for deletions:
  estimateSVSizes(n=20, minSize=500, maxSize=10000, hist=FALSE, default="deletions")

Budheimer/RSVSim documentation built on May 30, 2019, 1:26 p.m.