addMutCol: Adds mutation information to MAE

Description Usage Arguments Examples

View source: R/TCGA_pipe.R

Description

Adds mutation information to MAE

Usage

1
2
3
4
addMutCol(data, disease, genes,
  mutant_variant_classification = c("Frame_Shift_Del", "Frame_Shift_Ins",
  "Missense_Mutation", "Nonsense_Mutation", "Splice_Site", "In_Frame_Del",
  "In_Frame_Ins", "Translation_Start_Site", "Nonstop_Mutation"))

Arguments

data

MAE object

disease

TCGA disease (LUSC, GBM, etc)

genes

list of genes to add information

mutant_variant_classification

List of mutant_variant_classification that will be consider a sample mutant or not.

Examples

1
2
3
4
5
## Not run: 
 data <- ELMER:::getdata("elmer.data.example") # Get data from ELMER.data
 data <- addMutCol(data, "LUSC","TP53")

## End(Not run)

ELMER documentation built on Nov. 1, 2018, 2:13 a.m.