estimate Abundances from sonicated samples

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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

1
estAbund(locations, lengths, replicates = NULL, jackknife = F, kmax=0, ...)

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

...

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 ccberry@users.r-forge.r-project.org

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