falcon (version 0.2)

getChangepoints: Getting Change-points

Description

This function estimates the change-points where one or both parent-specific copy numbers change. It uses a circular binary segmentation approach to find change-points in a binomial mixture process. The output of the function is the set of locations of the break points. If the whole genome is analyzed, it is recommended to run this function chromosome by chromosome, and the runs on different chromosomes can be done in parallel to shorten the running time.

Usage

getChangepoints(readMatrix, verbose=TRUE, pOri=c(0.49,0.51), error=1e-5, maxIter=1000)

Arguments

readMatrix

A data frame with four columns: AN, BN, AT, BT.

verbose

Provide progress messages if it is TRUE. This argument is TRUE by default. Set it to be FALSE if you want to turn off the progress messages.

pOri, error, maxIter

Parameters used in estimating the success probabilities of the mixed binomial distribution. See the manuscript by Chen and Zhang for more details. "pOri" provides the initial success probabilities. The two values in pOri needs to be different. "error" provides the stopping criterion. "maxIter" is the maximum iterating steps if the stopping criterion is not achieved.

References

Hao Chen, John Bell, Nicolas Zavala, Hanlee Ji and Nancy Zhang. Allele-specific copy number profiling by next-generation DNA sequencing. Nucleic Acids Research, 2014.

See Also

getASCN

Examples

data(Example) 
# tauhat = getChangepoints(readMatrix)  # uncomment this to run the function. 
 # This example has 6309 variant loci and it took 94 seconds to run on a laptop with 
 # Intel Core i5-2410M processor.