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Last data update: 2014.03.03

R: Joint Segmentation on log2ratio and log2mBAF Dimensions

joint.segmentation

R Documentation

Joint Segmentation on log2ratio and log2mBAF Dimensions

Description

We employ the algorithm developed by (Zhang et al., 2010) to perform joint segmentation on log2ratio and log2mBAF dimensions. The function outputs the starting and ending points of each CNV segment as well as some summary statistics.

Usage

joint.segmentation(data, min.snps = 10, global.pval.cutoff = 1e-04, 
    max.chpts = 30, verbose = TRUE)

Arguments

`data`	a data frame containing log2ratio and log2mBAF data generated by `cnv.data`.
`min.snps`	the minimum number of probes a segment needs to span.
`global.pval.cutoff`	the p-value cut-off a (or a pair) of change points to be determined as significant in each cycle of joint segmentation.
`max.chpts`	the maximum number of change points to be detected for each chromosome.
`verbose`	logical. If more details to be output. Default is `TRUE`.

Value

A data frame containing the starting and ending points of each CNV segment as well as some summary statistics.

Author(s)

Zhongyang Zhang <zhongyang.zhang@mssm.edu>

References

Zhang, N. R., Siegmund, D. O., Ji, H., Li, J. Z. (2010) Detecting simultaneous changepoints in multiple sequences. Biometrika, 97:631–645.

Examples

data(seq.data)

## Not run: 
seq.segs <- joint.segmentation(data=seq.data, min.snps=10, 
                               global.pval.cutoff=1e-4, max.chpts=30, 
                               verbose=TRUE)

## End(Not run)

## how the joint segmentation results look like
data(seq.segs)
head(seq.segs)