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.
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.
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 <zhongyang.zhang@mssm.edu>
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)