estAbund: estimate Abundances from sonicated samples

In sonicLength: Estimating Abundance of Clones from DNA Fragmentation Data

Description

When one or more replicate samples are sonicated and the lengths for each integration site are recorded, it is of interest to estimate actual number of sonicants allowing for coincidentally equal lengths. A likelihood approach is used here.

Usage

estAbund(locations, lengths, replicates = NULL, jackknife = F, kmax=0,
min.length = 20, ...)

Arguments

locations	a vector of IDs for distinct locations
lengths	a vector of the corresponding lengths
replicates	an optional vector of the replicate sample ID
jackknife	Whether to do leave-one-out jackknife samples over the replicates
kmax	highest count to bother with when computing mass function for counts. All higher values are globbed together in the result. If kmax==0 don't compute
min.length	Least length expected for a fragment. Shorter lengths will not be permitted
...	Other arguments that may be passed along to functions that do the real work.

Details

This is a wrapper function for maxEM so study that function to see what is going on.

Value

a list with components

theta	estimated abundances
phi	estimated bin probabilities
var.theta	variances of theta
iter	number of iterations till convergence was achieved
call	the function call
lframe	the data.frame used to construct the estimate of phi
obs	the observed counts of distinct lengths
jackknife	a list of calls to maxEM with one replicate omitted in each
data	a data.frame with columns locations,lengths, and replicates (if supplied)

Author(s)

Charles C Berry [e-mail]

References

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.

See Also

maxEM phi.update.lframe The package vignette:Estimating Abundances with sonicLength

sonicLength documentation built on Sept. 20, 2021, 9:06 a.m.