sonicLength: Estimating Abundance of Clones from DNA fragmentation data

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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.

Author
Charles Berry <ccberry@ucsd.edu>
Date of publication
2014-08-24 10:56:28
Maintainer
Charles Berry <ccberry@ucsd.edu>
License
GPL (>= 2)
Version
1.4.4

View on CRAN

Man pages

A1
HTLV-1 Fragment Length Data
estAbund
estimate Abundances from sonicated samples
estep
E-Step for Abundance Estimation
maxEM
maximum likelihood estimates relative abundances
maxEM.iter.control
iteration controls
mstep
M-step to maximize theta
phi.update.lframe
estimate phi
simFragment
Simple Fragment Length Distribution
simSonic
Simulate Sonicated Data
sonicLength.start-package
Calibration of Number of Length Variants

Files in this package

sonicLength
sonicLength/inst
sonicLength/inst/CITATION
sonicLength/inst/doc
sonicLength/inst/doc/EstAbund.pdf
sonicLength/inst/doc/EstAbund.R
sonicLength/inst/doc/EstAbund.Rnw
sonicLength/NAMESPACE
sonicLength/data
sonicLength/data/A1.RData
sonicLength/R
sonicLength/R/mstep.R
sonicLength/R/simFragment.R
sonicLength/R/simSonic.R
sonicLength/R/pad.tab.R
sonicLength/R/mmN.R
sonicLength/R/maxEM.R
sonicLength/R/estep.R
sonicLength/R/estAbund.R
sonicLength/vignettes
sonicLength/vignettes/EstAbund.Rnw
sonicLength/MD5
sonicLength/build
sonicLength/build/vignette.rds
sonicLength/DESCRIPTION
sonicLength/man
sonicLength/man/A1.Rd
sonicLength/man/estep.Rd
sonicLength/man/maxEM.Rd
sonicLength/man/mstep.Rd
sonicLength/man/simFragment.Rd
sonicLength/man/sonicLength.start-package.Rd
sonicLength/man/estAbund.Rd
sonicLength/man/phi.update.lframe.Rd
sonicLength/man/maxEM.iter.control.Rd
sonicLength/man/simSonic.Rd