add_protein_change_column: Add protein change column.
In Bio-Core/BioCore.Annotation: BioCore Variant Annotation Package

Description Usage Arguments Author(s) Examples

View source: R/add_protein_change_column.R

Extract the protein change from the ANNOVAR string and put the value into it's own column.

1	add_protein_change_column(data = NULL)

data

dataframe containing the ANNOVAR output (required)

Richard J. de Borja <richard.deborja@uhnresearch.ca>

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (data = NULL)
{
    if (is.null(data))
        stop("Mandatory argument data is missing")
    data$aa_change <- apply(X = as.matrix(data$AAChange.refGene),
        MARGIN = 1, FUN = get_protein_change)
    data$aa_gene <- apply(X = as.matrix(data$AAChange.refGene),
        MARGIN = 1, FUN = get_gene_name)
    return(data)
  }