saasCNV (version 0.3.4)

joint.segmentation: 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.

References

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

See Also

cnv.data

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)