Description Usage Arguments Value Author(s) Examples
The effect of a splice variant is predicted for individual protein-coding transcripts.
1 2 | predictVariantEffects(sgv, tx, genome, fix_start_codon = TRUE,
output = c("short", "full"), cores = 1)
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sgv |
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tx |
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genome |
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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 |
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.
Leonard Goldstein
1 2 3 | require(BSgenome.Hsapiens.UCSC.hg19)
seqlevelsStyle(Hsapiens) <- "NCBI"
predictVariantEffects(sgv_pred, tx, Hsapiens)
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