a data frame constructed from a text file with LRR and BAF information.
output.dir
the directory to which all the results will be located.
sample.id
sample ID to be displayed in the data frame of the results and
the title of some diagnosis plots.
do.GC.adjust
logical. If GC content adjustment on log2ratio to be carried out.
Default is FALSE. See GC.adjust for details.
gc.file
the location of tab-delimit file with GC content (averaged per 1kb window)
information. See GC.adjust for details.
min.chr.probe
the minimum number of probes tagging a chromosome for it
to be passed to the subsequent analysis.
min.snps
the minimum number of probes a segment needs to span.
joint.segmentation.pvalue.cutoff
the p-value cut-off one (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.
do.merge
logical. If segments merging step to be carried out.
Default is TRUE.
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.
num.perm
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.cnvcall.on.merge
logical. If CNV call to be done for the segments after
merging step. Default is TRUE. If TRUE, CNV call will be done on the
segments resulting directly from joint segmentation without merging step.
cnvcall.pvalue.cutoff
a p-value cut-off for CNV calling.
do.boundary.refine
logical. If the segment boundaries based on the grid of
heterozygous probes to be refined by all probes with LRR data. Default is FALSE.
We do not recommend to perform this step except in the case that the segment
boundaries need to be aligned well on the same grid of probes for downstream analysis.
do.plot
logical. If diagnosis plots to be output. Default is TRUE.
cex
a numerical value giving the amount by which plotting text and
symbols should be magnified relative to the default. It can be adjusted
in order to make the plot legible.
ref.num.probe
integer. The reference number of probes against which
a segment is compared in order to determine the cex of the segment
to be displayed. Default is NULL. If NULL, It will be automatically
specified as 1/100 of the number of data points.
do.gene.anno
logical. If gene annotation step to be performed. Default is FALSE.
gene.anno.file
a tab-delimited file containing gene annotation information.
For example, RefSeq annotation file which can be found at UCSC genome browser.
seed
integer. Random seed can be set for reproducibility of results.
verbose
logical. If more details to be output. Default is TRUE.
Details
See the vignettes of the package for more details.
Value
The results, including visualization plots are placed in
subdirectories of the output directory output.dir
as specified by user.
Author(s)
Zhongyang Zhang <zhongyang.zhang@mssm.edu>
References
Zhongyang Zhang and Ke Hao. (2015) SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals
for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data.
PLoS Computational Biology, 11(11):e1004618.