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Data frame of accepted data names for standard genomic files. This serves as a dictionary to help disambiguate raw column names from user entered mutation, CNA or structural variant data

Usage

names_df

Format

A data frame

maf_column_name

data field names as they appear in common MAF file

api_column_name

data field names as they appear in common cBioPortal API retrieved files

mutation_input

does this field appear in mutation files?

fusion_input

does this field appear in mutation/sv files?

cna_input

does this field appear in CNA files?

definition

variable definition

notes

data notes

sc_maf_column_name

snake case version of maf_column_name

sc_api_column_name

snake case version of api_column_name

caps_maf_column_name

upper case version of maf_column_name

caps_api_column_name

upper case version of api_column_name

internal_column_name

name used for each field for all internal processing functions