casper (version 2.6.0)

txLength: ~~ Methods for Function txLength in Package casper ~~

Description

~~ Methods for function txLength in package casper ~~ Function to retrieve transcript lengths from annotated genome (class genomeDB).

Usage

txLength(islandid, txid, genomeDB)

Arguments

islandid

Retrieve length for transcripts in island islandid.

txid

Retrieve length for txid transcripts.

genomeDB

Annotated genome of class genomeDB.

Value

Named numeric vector with transcript lengths.

Methods

signature(islandid = "character", txid = "missing", genomeDB = "annotatedGenome")

Retrieve lengths from genomeDB for transcripts in islandid islands.

signature(islandid = "missing", txid = "character", genomeDB = "annotatedGenome")

Retrieve lengths from genomeDB for txid transcripts.

signature(islandid = "missing", txid = "missing", genomeDB = "annotatedGenome")

Retrieve or calculate lengths for all transcripts in the annotated genome genomeDB.

Details

When called for the first time lengths are calculated and stored in the object genomeDB. Subsequent calls refer to these computed values.