simSonic: Simulate Sonicated Data

In sonicLength: Estimating Abundance of Clones from DNA Fragmentation Data

Description

Sonication and Processing of DNA containing retroviral sequences yields genomic locations of retroviral insertion sites and a set of associated fragment lengths. The simulation depends on the expected number of fragments from each site and the distribution of lengths.

Usage

simSonic( theta, phi )

Arguments

theta	a vector of expected number of fragments from each site. If the vector has unqiue names, these will be used to label the locations
phi	a vector of probabilities (or a list containing a vector named phi) whose names are like 'rep len', where 'rep' defines the replicate and 'len' defines the sonicant length . More than one replicate can be used, In any case 1-exp(-phi%o%theta) determines the probability of observations in the different locaitons, of the different lengths, and in different replicates

Details

This object can provide the arguments used by estAbund

Value

a data.frame with columns locations, lengths, and replicates. See estAbund for more details.

Author(s)

Charles C. Berry [e-mail]

Examples

theta <- seq(0.5,20.5,by=0.5)
phi <- prop.table(1:10)
names(phi) <- paste( 1 , 51:60 )
res <- simSonic( theta, phi )
head(res)
tail(res)
summary(res)

sonicLength documentation built on Sept. 20, 2021, 3 a.m.