merging.segments {saasCNV} | R Documentation |
Merge Adjacent Segments
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 |
segs.stat |
a data frame containing segment locations and summary statistics
resulting from |
use.null.data |
logical. If only data for probes located in normal copy
segments to be used for bootstrapping. Default is |
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 |
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 |
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 |
seed |
integer. Random seed can be set for reproducibility of results. |
verbose |
logical. If more details to be output. Default is |
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
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)