annotate {SGSeq} | R Documentation

## Annotation with respect to transcript features

### Description

Features in `query` are assigned transcript names and gene names of structurally compatible features in `subject` (see below). If a feature in `query` does not match any features in `subject`, its geneName inherits from connected annotated features.

### Usage

    annotate(query, subject)

### Arguments

`query` | `SGFeatures`, `SGVariants`, `SGFeatureCounts` or `SGVariantCounts` object
`subject` | `TxFeatures` object

### Details

Feature matching is performed as follows: Query splice junctions are matched with identical subject splice junctions. Query splice sites are matched with splice sites implied by subject splice junctions. Query exon bins are matched with overlapping subject exons. Spliced boundaries of query exon bins must match spliced subject exon boundaries. Query exon bins cannot extend across spliced subject exon boundaries.

### Value

`query` with updated `txName`, `geneName` column slots

### Author(s)

Leonard Goldstein

### Examples

    sgf_annotated <- annotate(sgf_pred, txf_ann)
    sgv_annotated <- annotate(sgv_pred, txf_ann)

[Package SGSeq version 1.21.9 Index]