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.
estAbund(locations, lengths, replicates = NULL, jackknife = F, kmax=0,
min.length = 20, …)a vector of IDs for distinct locations
a vector of the corresponding lengths
an optional vector of the replicate sample ID
Whether to do leave-one-out jackknife samples over the replicates
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
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.
a list with components
estimated abundances
estimated bin probabilities
variances of theta
number of iterations till convergence was achieved
the function call
the data.frame used to construct the estimate of
phi
the observed counts of distinct lengths
a list of calls to maxEM with one replicate
omitted in each
a data.frame with columns
locations,lengths, and replicates (if supplied)
This is a wrapper function for maxEM so study that
function to see what is going on.
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.
maxEM
phi.update.lframe
The package vignette:Estimating Abundances with sonicLength