prepare_metabric_for_spongEffects: prepare METABRIC formats for spongEffects

View source: R/fn_spongeffects_utility.R

prepare_metabric_for_spongEffectsR Documentation

prepare METABRIC formats for spongEffects

Description

prepare METABRIC formats for spongEffects

Usage

prepare_metabric_for_spongEffects(
  metabric_expression,
  metabric_metadata,
  subtypes_of_interest,
  bioMart_gene_ensembl = "hsapiens_gene_ensembl",
  bioMart_gene_symbol_columns = "hgnc_symbol"
)

Arguments

metabric_expression

filepath to expression data in metabric format

metabric_metadata

filepath to metabric metadata in metabric format

subtypes_of_interest

array e.g., c("LumA", "LumB", "Her2", "Basal", "Normal")

bioMart_gene_ensembl

bioMart gene ensemble name (e.g., hsapiens_gene_ensembl). (See https://www.bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.html) (default: hsapiens_gene_ensembl)

bioMart_gene_symbol_columns

bioMart dataset column for gene symbols (e.g. human: hgnc_symbol, mouse: mgi_symbol) (default: hgnc_symbol)

Value

list with metabric expression and metadata. You can access it with list$objectname for further spongEffects steps


biomedbigdata/SPONGE documentation built on Feb. 6, 2023, 10:19 p.m.