SGSeq (version 1.4.0)

predictVariantEffects: Predict the effect of splice variants on protein-coding transcripts

Description

The effect of each splice variant is assessed with respect to individual protein-coding transcripts.

Usage

predictVariantEffects(sgv, tx, genome, summarize = TRUE, cores = 1)

Arguments

sgv

SGVariants object

tx

A TxDb object or GRangesList of exons grouped by transcript with metadata columns cdsStart and cdsEnd (by convention, cdsStart < cdsEnd for both strands). For import from GFF format, use function importTranscripts.

genome

BSgenome object

summarize

Logical indicating whether results should be summarized per variant

cores

Number of cores available for parallel processing

Value

For summarize = FALSE a data.frame with rows corresponding to a variant-transcript pair. The data.frame includes columns for variant identifier, transcript name, type of alteration, protein sequences for the reference transcript and the transcript variant, protein lengths and coordinates of the variant in the protein sequences. Start and end coordinates are 0- and 1-based, respectively, to allow for specification of deletions. For summarize = TRUE a character vector matching argument sgv with comma-separated predicted alterations for individual transcripts.

Examples

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