getMappedFeatures: Wrapper to get feature mappings.

In yigbt/multiGSEA: Combining GSEA-based pathway enrichment with multi omics data integration

Wrapper to get feature mappings.

Description

Feature mappings will be used from hard disk in case they have been mapped before and 'useLocal' is not set to be FALSE. In other cases, a feature extraction will be done and the results are stored for a following occasion.

Usage

getMappedFeatures(
  pathways,
  returnID = "SYMBOL",
  organism = "hsapiens",
  which = "proteins",
  useLocal = TRUE
)

Arguments

pathways	List of pathway definitions.
returnID	String specifying the returned ID format.
organism	String defining the organism of analysis.
which	Mode to extract the features, either \'proteins\' or \'metabolites\'.
useLocal	Boolean specifying whether or not to use the local preprocessed mapping.

Value

List of mapped features for an omics layer.

yigbt/multiGSEA documentation built on Nov. 25, 2024, 9:11 a.m.