predictVariantEffects {SGSeq} | R Documentation

## Predict the effect of splice variants on protein-coding transcripts

### Description

The effect of a splice variant is predicted for individual protein-coding transcripts.

### Usage

    predictVariantEffects(sgv, tx, genome, fix_start_codon = TRUE,
      output = c("short", "full"), cores = 1)

### Arguments

`sgv` | `SGVariants` object
`tx` | `TxDb` object, or `GRangesList` of exons grouped by transcript with metadata columns `txName`, `geneName`, `cdsStart` and `cdsEnd` (by convention, cdsStart < cdsEnd for both strands). For import from GFF format, use function `importTranscripts`.
`genome` | `BSgenome` object
`fix_start_codon` | Logical indicating whether the annotated start codon should be considered fixed and the variant transcript should not be scanned for alternative start codons
`output` | Character string indicating whether short results or full results (with additional columns) should be returned
`cores` | Number of cores available for parallel processing

### Value

`data.frame` with rows corresponding to a variant-transcript pair. The output includes columns for variant identifier, transcript name, gene name, type of alteration at the RNA and protein level, and variant description at the RNA and protein level in HGVS notation. For `output = "full"` additional columns are returned. These include the full-length RNA and protein sequence for the reference and variant transcript. Event start and end coordinates in the full output are 0- and 1-based, respectively (to allow for description of deletions). Coordinates for the last junction in a transcript refer to the last base of the second-to-last exon.

### Author(s)

Leonard Goldstein

### Examples

    require(BSgenome.Hsapiens.UCSC.hg19)
    seqlevelsStyle(Hsapiens) <- "NCBI"
    predictVariantEffects(sgv_pred, tx, Hsapiens)

[Package SGSeq version 1.28.0 Index]