A class to hold the read count data that is used by ExomeDepth to call CNVs.

Objects can be created by calls of the form ```
new("ExomeDepth",
data = NULL, test, reference, formula = 'cbind(test, reference) ~
1', subset.for.speed = NULL)
```

.
`data`

is optional and is only used if the `formula`

argument refers to covariates (in which case these covariates must be
included in the data frame).
`test`

and `reference`

refer to the read count data for the
test and reference samples.
Creating a ExomeDepth object will automatically fit the beta-binomial
model (using routines from the `aod`

package) and compute the
likelihood for the three copy number states (normal, deletion and
duplication).

`test`

:`numeric`

, read count data for the test sample.`reference`

:`numeric`

, read count data for the reference sample (usually a combination of samples).`formula`

:`character`

, a character string describing the linear model linking test and reference. Typically this would be`cbind(test, reference) ~ 1`

.`expected`

:The expected read count data for the test sample assuming normal copy number.

`phi`

:The over-dispersion parameter of the binomial model. See the

`aod`

package for more details.`likelihood`

:A matrix of likelihood values, one column per copy number (deletion, normal, duplication).

`annotations`

:A

`data.frame`

specifying the chromosome, start and end for the bins used in the read count computation.`CNV.calls`

:A

`data.frame`

describing the output of the CNV calling procedure.

- CallCNVs
`signature(x = "ExomeDepth", transition.probability = "numeric", chromosome = "factor", start = "numeric", end = "numeric", name = "character") )`

: Uses the pre-computed likelihood values and fits a hidden Markov Chain to the data to generated merged CNV calls.- AddAnnotations
`signature(object = "ExomeDepth", name = "character", chromosome = "factor", start = "numeric", end = "numeric")`

: This method is unlikely to be directly used but it can include the exon names, chromosome, start, end into the ExomeDepth object.- TestCNV
`signature(x = "ExomeDepth", chromosome = "factor", start = "numeric", end = "numeric", type = "character")`

: type must be either deletion of duplication. This function takes an ExomeDepth object and returns the Bayes factor in favor of a CNV at the specified location.

Vincent Plagnol

Paper recently submitted

`select.reference.set`

`CallCNVs`

`aod`

1 | ```
showClass("ExomeDepth")
``` |

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