Description Usage Arguments Details Value Author(s) See Also Examples
Assign SCNA state to each segment directly from joint segmentation or from the results after segments merging step.
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data |
a data frame containing log2ratio and log2mBAF data generated
by |
sample.id |
sample ID to be displayed. |
segs.stat |
a data frame containing segment locations and summary statistics
resulting from |
maxL |
integer. The maximum length in terms of number of probes a bootstrapped segment
may span. Default is |
N |
the number of replicates drawn by bootstrap. |
pvalue.cutoff |
a p-value cut-off for CNV calling. |
seed |
integer. Random seed can be set for reproducibility of results. |
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 |
The baseline adjustment step is incorporated implicitly in the function.
A few more columns have been add to the data frame resulting from
joint.segmentation
or merging.segments
,
which summarize the baseline adjusted median log2ratio, log2mBAF,
p-values and CNV state for each segment.
Zhongyang Zhang <zhongyang.zhang@mssm.edu>
joint.segmentation
, merging.segments
, cnv.data
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