CRAN/E | sonicLength

sonicLength

Estimating Abundance of Clones from DNA Fragmentation Data

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About

Estimate the abundance of cell clones from the distribution of lengths of DNA fragments (as created by sonication, whence ‘sonicLength’). The algorithm in "Estimating abundances of retroviral insertion sites from DNA fragment length data" by Berry CC, Gillet NA, Melamed A, Gormley N, Bangham CR, Bushman FD. Bioinformatics; 2012 Mar 15;28(6):755-62 is implemented. The experimental setting and estimation details are described in detail there. Briefly, integration of new DNA in a host genome (due to retroviral infection or gene therapy) can be tracked using DNA sequencing, potentially allowing characterization of the abundance of individual cell clones bearing distinct integration sites. The locations of integration sites can be determined by fragmenting the host DNA (via sonication or fragmentase), breaking the newly integrated DNA at a known sequence, amplifying the fragments containing both host and integrated DNA, sequencing those amplicons, then mapping the host sequences to positions on the reference genome. The relative number of fragments containing a given position in the host genome estimates the relative abundance of cells hosting the corresponding integration site, but that number is not available and the count of amplicons per fragment varies widely. However, the expected number of distinct fragment lengths is a function of the abundance of cells hosting an integration site at a given position and a certain nuisance parameter. The algorithm implicitly estimates that function to estimate the relative abundance.

Citation sonicLength citation info

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Version 1.4.7
R ≥ 2.14.0
Published 2021-09-20 1115 days ago
Needs compilation? no
License GPL-2
License GPL-3
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Maintainer

Maintainer

Charles Berry

Authors

Charles Berry

Material

Reference manual
Package source

Vignettes

Estimating Abundances with sonicLength

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

sonicLength archive

Depends

R ≥ 2.14.0
splines

Reverse Imports

hiReadsProcessor