SGVariants {SGSeq} | R Documentation

## Splice graph variants

### Description

Creates an instance of S4 class `SGVariants` for storing splice variants.

### Usage

    SGVariants(x)

### Arguments

`x` | `GRangesList` of `SGFeatures` with appropriate outer metadata columns

### Details

`SGVariants` includes columns as described below.

- `from` and `to` indicate the variant start and end, respectively. `from` nodes are splice donors (“D”) or transcript starts (“S”). `to` nodes are splice acceptors (“A”) or transcript ends (“E”).

- `type` and `featureID` describe the variant in terms of the splice graph features that make up the variant.

- `segmentID` specifies unique identifiers labelling unbranched segments of the splice graph.

- `closed5p` indicates whether nodes in the variant can be reached from nodes outside of the variant exclusively through the `from` node.

- `closed3p` indicates whether nodes in the variant can reach nodes outside of the variant exclusively through the `to` node.

- `closed5pEvent` indicates whether nodes in the event can be reached from nodes outside of the event exclusively through the `from` node.

- `closed3pEvent` indicates whether nodes in the event can reach nodes outside of the event exclusively through the `to` node.

- `geneID` has the same interpretation as for `SGFeatures`.

- `eventID` and `variantID` are unique identifiers for each event and variant, respectively.

- `featureID5p` and `featureID3p` indicate representative features used for variant quantification at the start and end of the variant, respectively.

- `featureID5pEvent` and `featureID3pEvent` indicate the ensemble of representative features at the start and end of the event, respectively.

- `txName` indicates structurally compatible transcripts.

- `geneName` behaves as for `SGFeatures`.

- `variantType` indicates whether a splice variant is consistent with a canonical splice event (for a list of possible values, see the manual page for `annotateSGVariants`).

- `variantName` provides a unique name for each splice variant (for details, see the manual page for `makeVariantNames`).

### Value

`SGVariants` object

### Author(s)

Leonard Goldstein

### Examples

    sgv <- SGVariants()

[Package SGSeq version 1.20.0 Index]