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| ExomeCNV-package | Exome Sequencing-Based CNV and LOH Detection. |
| 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. |
| chr.median | Calculate log ratio of depth of coverage between paired samples. |
| classify.eCNV | Call CNV on each exon based on log ratio of read depth. |
| classify.logR | Call CNV on each exon based on log ratio of read depth. |
| CNV.analyze | A wrapper function of DNAcopy that prepare input and run CBS. |
| cnv.points | Plot CNV calls over log ratio. |
| colors | Constants used in the package. |
| combine.baf | Use Circular Binary Segmentation to create segments and call LOH on each segment based on BAF using specified method. |
| combine.CNV | Combine results of DNAcopy and classify.eCNV into one table. |
| combine.LOH | Use Circular Binary Segmentation to create segments and call LOH on each segment based on BAF using specified method. |
| COVERAGE_HEADER | Constants used in the package. |
| do.DNAcopy | Use Circular Binary Segmentation to create segments and call LOH on each segment based on BAF using specified method. |
| do.merge.cnv.intervals | Combine results of DNAcopy and classify.eCNV into one table. |
| do.merge.loh.intervals | Use Circular Binary Segmentation to create segments and call LOH on each segment based on BAF using specified method. |
| do.plot.eCNV | Plot CNV calls over log ratio. |
| do.plot.loh | Plot output of LOH calls. |
| do.plot.one.eCNV | Plot CNV calls over log ratio. |
| do.plot.one.loh | Plot output of LOH calls. |
| ExomeCNV | Exome Sequencing-Based CNV and LOH Detection. |
| expand.loh | Propagate LOH calls to all heterozygous positions within each LOH segment. |
| find.max.of.2lists | Pooling a compendium of "normal" exome samples. |
| find.min.of.2lists | Call LOH on each heterozygous position using specified test statistic. |
| get.alpha | Calculate theoretical specificity, sensitivity, area under curve (AUC). |
| get.alpha.inv | Calculate theoretical specificity, sensitivity, area under curve (AUC). |
| get.AUC | Calculate theoretical specificity, sensitivity, area under curve (AUC). |
| get.end.position | Call LOH on each heterozygous position using specified test statistic. |
| get.power | Calculate theoretical specificity, sensitivity, area under curve (AUC). |
| get.power.inv | Calculate theoretical specificity, sensitivity, area under curve (AUC). |
| get.proper.cnv.positions | A wrapper function of DNAcopy that prepare input and run CBS. |
| get.r.cutoff | Call CNV on each exon based on log ratio of read depth. |
| get.sensitivity | Calculate theoretical specificity, sensitivity, area under curve (AUC). |
| get.specificity | Calculate theoretical specificity, sensitivity, area under curve (AUC). |
| good.percent | Constants used in the package. |
| guesstimate.contamination | Estimate admixture/contamination rate in a sample. |
| guesstimate.contarmination | Estimate admixture/contamination rate in a sample. |
| LOH.analyze | Call LOH on each heterozygous position using specified test statistic. |
| make.chunk | Combine results of DNAcopy and classify.eCNV into one table. |
| make.loh.chunk | Use Circular Binary Segmentation to create segments and call LOH on each segment based on BAF using specified method. |
| make.loh.strata | Use Circular Binary Segmentation to create segments and call LOH on each segment based on BAF using specified method. |
| MIL | Constants used in the package. |
| 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. |
| my.cols | Combine results of DNAcopy and classify.eCNV into one table. |
| normalize.logR | Calculate log ratio of depth of coverage between paired samples. |
| one.sample.loh.test | Call LOH on each heterozygous position using specified test statistic. |
| phalfnorm | Call LOH on each heterozygous position using specified test statistic. |
| pool.coverage | Pooling a compendium of "normal" exome samples. |
| pool.coverage.from.files | Pooling a compendium of "normal" exome samples. |
| r.cutoffs | Constants used in the package. |
| RBIND_LIM | Constants used in the package. |
| 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(). |
| read.gtf | Read coverage file in GTF format as created by Howie Goodell. |
| rho.list | Constants used in the package. |
| save.logR | Save logR in files by chromosome. |
| strip.chr.name | A wrapper function of DNAcopy that prepare input and run CBS. |
| test.num.copy | Constants used in the package. |
| two.sample.loh.CMH.test | Call LOH on each heterozygous position using specified test statistic. |
| two.sample.loh.deviation.test | Call LOH on each heterozygous position using specified test statistic. |
| two.sample.loh.test | Call LOH on each heterozygous position using specified test statistic. |
| window.sizes | Constants used in the package. |
| write.loh.output | Generate an output file for LOH calls. |
| write.output | Generate output files from ExomeCNV outputs. |