sonicLength.start-package: Calibration of Number of Length Variants
In sonicLength: Estimating Abundance of Clones from DNA Fragmentation Data

Description Details Author(s) References

Estimate the number of fragments produced by sonication of integration sites in DNA (as arise in gene therapy or in retroviral infections) from tallies of the number of distinct lengths. See the Berry et al. reference where the experimental setting and algorithm are spelled out in detail.

Package:	sonicLength
Type:	Package
License:	see file LICENSE distributed with this software
LazyLoad:	yes

This package has the necessary utilities to provide a function that will do calibration of the number of distinct lengths (for an integration site recovered via sonication) to estimate the number of distinct sonication fragments that underlie the observed number of lengths.

Charles C. Berry

Maintainer: <ccberry@ucsd.edu>

The reference to the algorithm is:

Estimating abundances of retroviral insertion sites from DNA fragment length data. Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62.

Some applications that illustrate use of this method are found here:

Gillet, Nicolas A., et al. "The host genomic environment of the provirus determines the abundance of HTLV-1 infected T-cell clones." Blood 117.11 (2011): 3113-3122.

Maldarelli, F., et al. "Specific HIV integration sites are linked to clonal expansion and persistence of infected cells." Science 345.6193 (2014): 179-183.

sonicLength documentation built on Sept. 20, 2021, 3 a.m.