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| ExomeDepth-package | Read depth based CNV calls for exome DNA sequence data |
| AddAnnotations-method | Class 'ExomeDepth' |
| AnnotateExtra | Add annotations to a ExomeDepth object |
| AnnotateExtra-method | Additional annotations for ExomeDepth objects |
| AnnotateExtra-methods | Additional annotations for ExomeDepth objects |
| CallCNVs | Call CNV data from an ExomeDepth object. |
| CallCNVs-method | Class 'ExomeDepth' |
| Conrad.hg19.common.CNVs | Conrad et al common CNVs |
| count.everted.reads | Count the number of everted reads for a set of BAM files. |
| countBam.everted | Counts everted reads from a single BAM file |
| countBamInGRanges.exomeDepth | Compute read count data from BAM files. |
| ExomeCount | Example dataset for ExomeDepth |
| ExomeDepth | Read depth based CNV calls for exome DNA sequence data |
| ExomeDepth-class | Class 'ExomeDepth' |
| exons.hg19 | Positions of exons on build hg19 of the human genome |
| exons.hg19.X | Positions of exons on build hg19 of the human genome and on chromosome X |
| genes.hg19 | Positions of genes on build hg19 of the human genome |
| get.power.betabinom | Estimate the power to compare two beta-binomial distributions. |
| getBamCounts | Get count data for multiple exomes |
| initialize-method | ~~ Methods for Function 'initialize' ~~ |
| initialize-methods | ~~ Methods for Function 'initialize' ~~ |
| plot-method | Plotting function for ExomeDepth objects |
| plot-methods | Plotting function for ExomeDepth objects |
| plot.ExomeDepth | Plotting function for ExomeDepth objects |
| qbetabinom | Quantile for betabin function |
| qbetabinom.ab | Quantile function for the beta-binomial distribution |
| select.reference.set | Combine multiple samples to optimize the reference set in order to maximise the power to detect CNV. |
| show-method | ~~ Methods for Function 'show' ~~ |
| show-methods | ~~ Methods for Function 'show' ~~ |
| somatic.CNV.call | Call somatic variants between healthy and disease tissues. |
| TestCNV | Computes the Bayes Factor in favour of a CNV defined by position and type. |
| TestCNV-method | Class 'ExomeDepth' |
| viterbi.hmm | Computes the Viterbi path for a hidden markov model |