denovoGeneExpr-class {casper} | R Documentation

## Class "denovoGeneExpr"

### Description

`denovoGeneExpr` stores inferred expression for de novo splicing variants for a single gene. `denovoGenomeExpr` stores the information for several genes (typically, the whole genome).

### Objects from the Class

Objects are returned by `calcDenovo`. When running `calcDenovo` on multiple genes results are returned in a `denovoGenomeExpr` object. Results for a single gene can be retrieved using the [[ operator as usual, which returns a `denovoGeneExpr` object.

### Slots

posprob

  `data.frame` containing the posterior probability of each model

expression

  `data.frame` with the estimated expression of each variant under each model

variants

  `matrix` indicating the exons contained in each variant.

integralSum

  Sum of the log(integrated likelihood) + log(model prior probability) across all considered models.

npathDeleted

  Number of paths that had 0 probability under all considered variants and had to be excluded for model fitting purposes.

priorq

  Input parameter to `calcDenovo`

txLength

  Length of transcripts in bp (including new isoforms found by casper)

### Methods

show

  `signature(object = "denovoGeneExpr")`: Displays general information about the object.

names

  Show names (island ids)

"["

  Selects a subset of genes

"[["

  Selects a single gene

posprob

  Accesses the posterior probabilities of each model (slot posprob)

variants

  Accesses the variant names and their respective exons

variants<-

  Replaces the value of the slot variants (can be useful for renaming variants, for instance)

### Author(s)

David Rossell

### See Also

`calcDenovo` to create objects from the class. `denovoExpr` to obtain expression estimates from `denovoGenomeExpr` objects.

### Examples

    showClass("denovoGeneExpr")

[Package casper version 2.20.0 Index]