pathCounts-class: Class "pathCounts"

In casper: Characterization of Alternative Splicing based on Paired-End Reads

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")

casper documentation built on Dec. 17, 2020, 2:01 a.m.