prepare_metabric_for_spongEffects: prepare METABRIC formats for spongEffects

In biomedbigdata/SPONGE: Sparse Partial Correlations On Gene Expression

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.