merging.segments: Merge Adjacent Segments

In saasCNV: Somatic Copy Number Alteration Analysis Using Sequencing and SNP Array Data

Description

It is an option to merge adjacent segments, for which the median values in either or both log2ratio and log2mBAF dimensions are not substantially different. For WGS and SNP array, it is recommended to do so.

Usage

merging.segments(data, segs.stat, use.null.data = TRUE, 
               N = 1000, maxL = NULL, merge.pvalue.cutoff = 0.05, 
               do.manual.baseline=FALSE,
               log2mBAF.left=NULL, log2mBAF.right=NULL, 
               log2ratio.bottom=NULL, log2ratio.up=NULL,
               seed = NULL, 
               verbose = TRUE)

Arguments

data	a data frame containing log2ratio and log2mBAF data generated by cnv.data.
segs.stat	a data frame containing segment locations and summary statistics resulting from joint.segmentation.
use.null.data	logical. If only data for probes located in normal copy segments to be used for bootstrapping. Default is TRUE. If a more aggressive merging is needed, it can be switched to FALSE.
N	the number of replicates drawn by bootstrap.
maxL	integer. The maximum length in terms of number of probes a bootstrapped segment may span. Default is NULL. If NULL, It will be automatically specified as 1/100 of the number of data points.
merge.pvalue.cutoff	a p-value cut-off for merging. If the empirical p-value is greater than the cut-off value, the two adjacent segments under consideration will be merged.
do.manual.baseline	logical. If baseline adjustment to be done manually. Default is FALSE.
log2mBAF.left, log2mBAF.right, log2ratio.bottom, log2ratio.up	left, right, bottom and up boundaries to be specified manually by a visual inspectio of 2-D diagnosis plot generated by diagnosis.cluster.plot. These parameters are active when do.manual.baseline=TRUE.
seed	integer. Random seed can be set for reproducibility of results.
verbose	logical. If more details to be output. Default is TRUE.

Value

A data frame with the same columns as the one generated by joint.segmentation.

Author(s)

Zhongyang Zhang <[e-mail]>

See Also

cnv.data, joint.segmentation

Examples

data(seq.data)
data(seq.segs)

## Not run: 
seq.segs.merge <- merging.segments(data=seq.data, segs.stat=seq.segs, 
                                 use.null.data=TRUE,
                                 N=1000, maxL=2000, 
                                 merge.pvalue.cutoff=0.05, verbose=TRUE)

## End(Not run)

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

saasCNV documentation built on May 1, 2019, 7:49 p.m.