transcripts {casper} | R Documentation

## Extracts transcript information (exon start and ends) from an `annotatedGenome` object, either for all transcripts or only those corresponding to a given island or transcript.

### Description

annotatedGenome objects store information regarding genes and transcripts. When there's an overlap in exons between several genes, these genes are grouped into gene islands.

`transcripts` retrieves all stored transcripts for a given transcript or island.

`matchTranscripts` finds transcripts in queryDB matching a transcript in subjectDB. The best match for each transcript in subjectDB is returned, unless difference in bp is >maxbp

### Usage

    transcripts(genomeDB, txid, islandid)

    matchTranscripts(queryDB, subjectDB, maxbp=10)

### Arguments

`genomeDB` | Object of class `annotatedGenome`
`txid` | Character indicating transcript identifier (optional)
`islandid` | Character indicating island identifier (optional)
`queryDB` | `annotatedGenome` with query transcripts
`subjectDB` | `annotatedGenome` with potentially matching transcripts
`maxbp` | Maximum difference in bp for transcripts to be matched

### Value

`IRangesList` where each element in the list corresponds to a different transcript.

### Methods

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

  Return exons for all transcripts in `genomeDB`

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

  Return exons for transcript `txid`

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

  Return exons for all transcripts in island `islandid`

### See Also

`genePlot` to plot the resulting transcripts

### Examples

    data(hg19DB)
    txs <- transcripts(txid="NM_005158",genomeDB=hg19DB)
    txs

[Package casper version 2.24.2 Index]