SGSeq (version 1.6.2)

predictVariantEffects: 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.

Examples

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