filterPathwaysByAnalyteCount: filterPathwaysByAnalyteCount utility method filtered a...

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

filterPathwaysByAnalyteCount utility method filtered a dataframe based on the number of analytes associated with rampPathwayIds contained in the dataframe. Like fisher exact code, this one retains pathways with analyte count >= min_path_size, and having analyte_count < max_path_size

Description

filterPathwaysByAnalyteCount utility method filtered a dataframe based on the number of analytes associated with rampPathwayIds contained in the dataframe. Like fisher exact code, this one retains pathways with analyte count >= min_path_size, and having analyte_count < max_path_size

Usage

filterPathwaysByAnalyteCount(
  db = RaMP(),
  pathway_dataframe,
  pathway_ramp_id_col_name = "pathwayRampId",
  min_path_size = 5,
  max_path_size = 150
)

Arguments

db	a RaMP databse object
pathway_dataframe	a dataframe containing at least one column that contains rampPathwayIds
pathway_ramp_id_col_name	the column name containing the rampPathwayIds
min_path_size	the minimum number of pathway members (genes and metabolites) to include the pathway in the output (default = 5)
max_path_size	the maximum number of pathway memnbers (genes and metaboltes) to include the pathway in the output (default = 150)

ncats/RaMP-DB documentation built on June 1, 2024, 9:34 p.m.