sonicLength: Estimating Abundance of Clones from DNA fragmentation data
Version 1.4.4

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.

AuthorCharles Berry <ccberry@ucsd.edu>
Date of publication2014-08-24 20:23:38
MaintainerCharles Berry <ccberry@ucsd.edu>
LicenseGPL (>= 2)
Version1.4.4
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("sonicLength", repos="http://R-Forge.R-project.org")

Popular man pages

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
See all...

All man pages Function index File listing

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

Functions

A1 Man page
EdL2.dlambda Source code
Ey.given.x Man page Source code
dfrag Man page Source code
estAbund Man page Source code
info.blocks Source code
maxEM Man page Source code
maxEM.iter.control Man page Source code
mmN Source code
mstep Man page Source code
pad.tab Source code
pfrag Man page Source code
phi.deriv.default Source code
phi.update.default Source code
phi.update.lframe Man page Source code
pr.y.given.x Man page Source code
qfrag Man page Source code
rfrag Man page Source code
simSonic Man page Source code
sonicLength Man page
sonicLength-package Man page
var.theta Source code

Files

DESCRIPTION
NAMESPACE
R
R/estAbund.R
R/estep.R
R/maxEM.R
R/mmN.R
R/mstep.R
R/pad.tab.R
R/simFragment.R
R/simSonic.R
build
build/vignette.rds
data
data/A1.RData
inst
inst/CITATION
inst/doc
inst/doc/EstAbund.R
inst/doc/EstAbund.Rnw
inst/doc/EstAbund.pdf
man
man/A1.Rd
man/estAbund.Rd
man/estep.Rd
man/maxEM.Rd
man/maxEM.iter.control.Rd
man/mstep.Rd
man/phi.update.lframe.Rd
man/simFragment.Rd
man/simSonic.Rd
man/sonicLength.start-package.Rd
vignettes
vignettes/EstAbund.Rnw
sonicLength documentation built on May 21, 2017, 4:06 a.m.

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