addMutCol: Adds mutation information to MAE

In ELMER: Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Description

Adds mutation information to MAE

Usage

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

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

## End(Not run)

ELMER documentation built on Nov. 8, 2020, 4:59 p.m.