Man pages for ExomeDepth
Calls Copy Number Variants from Targeted Sequence Data
| AnnotateExtra-ExomeDepth-method | AnnotateExtra |
| CallCNVs-ExomeDepth-method | CallCNVs |
| C_hmm | C_hmm |
| Conrad.hg19.common.CNVs | Conrad et al common CNVs |
| countBam.everted | Counts everted reads from a single BAM file |
| countBamInGRanges.exomeDepth | Compute read count data from BAM files. |
| count.everted.reads | Count the number of everted reads for a set of BAM files. |
| ExomeCount | Example dataset for ExomeDepth |
| 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... |
| genes.hg19 | Positions of genes on build hg19 of the human genome |
| getBamCounts | Get count data for multiple exomes |
| get_loglike_matrix | get_loglike_matrix |
| get.power.betabinom | Estimate the power to compare two beta-binomial... |
| initialize-ExomeDepth-method | ExomeDepth initialization tool |
| plot-methods | 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... |
| somatic.CNV.call | somatic.CNV.call |
| TestCNV-ExomeDepth-method | TestCNV |
| viterbi.hmm | Computes the Viterbi path for a hidden markov model |
