pathCounts-class {casper} | R Documentation

## Class "pathCounts"

### Description

Stores exon path counts.

### Objects from the Class

Objects are created with a call to `pathCounts`.

### Slots

counts

  List with one element per gene island. For each island, it contains a named vector with exon path counts. The names indicate the visited exons.

  For instance, consider that for gene '1' with 2 exons we observe 10 reads in which the left end falls completely in exon 1 and the right end in exon 2. Suppose that for 5 reads the left end bridges exons 1-2 and the right end falls in exon 2. Then `pc[['1']]` would contain `c(10,5)` and `names(pc[['1']])` would contain `c(".1-2.",".1.2-2.")`

denovo

  Logical variable. `FALSE` indicates that the counts correspond to a known genome (i.e. created with `procGenome`), and `TRUE` to a de novo annotated genome (i.e. created with `createDenovoGenome`).

stranded

  Logical variable. `TRUE` indicates that the path counts were obtained from and RNA-seq experiment where strand information was preserved.

### Methods

show

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

### Author(s)

Camille Stephan-Otto Attolini

### Examples

    showClass("pathCounts")

[Package casper version 2.20.0 Index]