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.
1 |
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 |
... |
Other arguments that may be passed along to functions that do the real work. |
This is a wrapper function for maxEM
so study that
function to see what is going on.
a list with components
theta |
estimated abundances |
phi |
estimated bin probabilities |
var.theta |
variances of |
iter |
number of iterations till convergence was achieved |
call |
the function call |
lframe |
the |
obs |
the observed counts of distinct lengths |
jackknife |
a list of calls to |
data |
a |
Charles C Berry ccberry@users.r-forge.r-project.org
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
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
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