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Annotate meta-programs with Bagaev TME subtypes

annotate_metaprograms_TME.Rd

Assigns each meta-program a TME subtype (IE, IE/F, F, D) by majority vote across the TCGA factors that were mapped to it.

Usage

annotate_metaprograms_TME(meta_programs_df, factor_tme_df, factors_mp_df)

Arguments

meta_programs_df

Data frame output of derive_meta_programs(), with columns meta_program and hallmarks.

factor_tme_df

Data frame output of map_factors_to_TME(), with columns factor and best_MFP.

factors_mp_df

Data frame output of map_factors_to_metaprograms() run on the TCGA factors themselves, with columns factor and best_MP.

Value

meta_programs_df with an additional TME_subtype column.