getVEPFromHGVS: getVEPFromHGVS

Description Usage Arguments Value Examples

Description

Function to get raw cDNA (CDS) from Ensembl REST API

Usage

1
2
3
getVEPFromHGVS(hgvsTag, transcriptID, idIncludedInTag = F,
  args = "canonical=1", includeOnlyCanonicalTranscript = F,
  outputDataFrame = F, verbose = F)

Arguments

hgvsTag

Character string with mutation HGVS Code

idIncludedInTag

Does hgvsTag have form ENSTxxx:c.156T>A or just the hgvs code?

args

Extra args to pass to VEP API request.

includeOnlyCanonicalTranscript

Only output canonical transcript data. default to FALSE

outputDataFrame

Flag to indicate whether data frame or list is output. Defaults to FALSE

verbose

Output verbose data for debugging

tag

Character string with ENST tag to get sequence for

Value

Request from VEP API

Examples

1
seq <- getVEPFromHGVS('c.1559delT','ENST00000343536')

gdelangel/genomicRTools documentation built on May 16, 2019, 11:14 p.m.