makeTmodFromDataFrame: Convert a data frame to a tmod object

In january3/tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

Convert a data frame to a tmod object

Description

Convert a data frame to a tmod object

Usage

makeTmodFromDataFrame(
  df,
  feature_col = 1,
  module_col = 2,
  title_col = NULL,
  extra_module_cols = NULL,
  extra_gene_cols = NULL
)

Arguments

df	A data frame
feature_col	Which column contains the feature (gene) IDs
module_col	Which column contains the module (gene set) IDs
title_col	Description of the modules (if NULL, the description will be taken from the module_col)
extra_module_cols	Additional columns to include in the module data frame
extra_gene_cols	Additional gene columns to include in the genes data frame

Details

'makeTmodFromFeatureDataFrame' converts mapping information from features (genes) to modules (gene sets). The data frame has a row for each feature-module pair.

'makeTmodFromModuleDataFrame' converts mapping information from features (genes) to modules (gene sets). The data frame has a row for each module, and all gene IDs corresponding to a module are stored as a comma separated string, e.g.

Vice versa, 'tmod2DataFrame' converts a tmod object to a data frame.

Value

A tmod object

See Also

makeTmodGS, makeTmodGS

Examples

df <- data.frame(
gene_id=LETTERS[1:10],
geneset_id=rep(letters[1:2], each=5),
geneset_description=rep(paste0("Gene set ", letters[1:2]), each=5))
res <- makeTmodFromDataFrame(df, 
  feature_col="gene_id", 
  module_col="geneset_id",
  title_col="geneset_description")

january3/tmod documentation built on Jan. 21, 2025, 11:07 a.m.