CNV.analyze             A wrapper function of DNAcopy that prepare
                        input and run CBS.
ExomeCNV-package        Exome Sequencing-Based CNV and LOH Detection.
LOH.analyze             Call LOH on each heterozygous position using
                        specified test statistic.
calculate.logR          Calculate log ratio of depth of coverage
                        between paired samples.
chr.hash                a data.frame of chromosome names to hash to
                        numeric representation.
classify.eCNV           Call CNV on each exon based on log ratio of
                        read depth.
colors                  Constants used in the package.
combine.CNV             Combine results of DNAcopy and classify.eCNV
                        into one table.
do.plot.eCNV            Plot CNV calls over log ratio.
do.plot.loh             Plot output of LOH calls.
expand.loh              Propagate LOH calls to all heterozygous
                        positions within each LOH segment.
get.AUC                 Calculate theoretical specificity, sensitivity,
                        area under curve (AUC).
guesstimate.contamination
                        Estimate admixture/contamination rate in a
                        sample.
multi.CNV.analyze       Use Circular Binary Segmentation to create
                        segments and call CNV on each segment.
multi.LOH.analyze       Use Circular Binary Segmentation to create
                        segments and call LOH on each segment based on
                        BAF using specified method.
pool.coverage           Pooling a compendium of "normal" exome samples.
read.all.coverage       Read all coverage files by chromosome.
read.coverage.gatk      Read coverage file produced by The Genome
                        Analysis Toolkit (GATK).
read.coverage.gtf       Read coverage file in GTF format as created by
                        Howie Goodell.
read.eCNV               Read all .RData files produced by
                        classify.eCNV().
save.logR               Save logR in files by chromosome.
write.loh.output        Generate an output file for LOH calls.
write.output            Generate output files from ExomeCNV outputs.
