convert_varclass: convert_varclass
In ahmetz/oncoPrintr: Create oncoPrints Based on Genomic Data

Description Usage Arguments Details Value Examples

View source: R/convert_varclass.R

if conversion of variant classes is selected, this function will do that

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convert_varclass(df, class_lookup = c(splicing = "Splicing", stop =
  "Nonsense", nonsynonymous = "Missense", nonframeshift = "InFrame", frameshift
  = "Frameshift", upstream = "Promoter", IntragenicDeletion = "Deletion"))

`df`	dataframe of genomic alterations

variant classes are converted based on this schema:
splicing -> Splicing
stopgain or stoploss -> Nonsense
nonsynonymous -> Missense
frameshift_deletion or insertion -> Frameshift
nonframeshift_deletion or insertion -> InFrame
upstream - Promoter
IntragenicDeletion -> Frameshift

data frame with variant classes converted