import_model_data: Perform common steps needed for importing model data

In Benjamin-Vincent-Lab/binfotron: Binfotron Bioinformatics Analysis Tools Suite

Perform common steps needed for importing model data

Description

All models will start with a matrix of ranked features, and the feature values of the features. This fxn orders the features, pulls out the top x and outputs disc and validation dataset matrices with the correct indep and dep variables. This function has the option to specify certain features or to pull the top x feature from a columns ranks file.

Usage

import_model_data(
  import_paths,
  df_filters = c(),
  ranks_feature_path = NULL,
  ranks_clm = NULL,
  ranks_count = NULL,
  set_clm = "Set",
  sample_key = binfotron::get_default_sample_key(),
  indep_vars = NULL,
  clinical_vars = NULL,
  dep_vars = NULL
)

Arguments

import_paths	Vector of paths to import and merge
df_filters	Character vector to be parsed in a loop using dplyr::filter
ranks_feature_path	Path to data matrix with feature names in one column and ranks in another.
ranks_clm	String to indicate which column contains the column ranks
ranks_count	Integer to indicate how many features to take from the column ranks
set_clm	Column name to indicate which samples are in "Validation" vs "Discovery" sets
sample_key	Column name to use as the sample key to merge all matrices
indep_vars	Character string of column names for the independent variables
clinical_vars	Character string of column names for the clinical variables. These will be added on in addition to the indep_vars.
dep_vars	Character string of column names for the dependent variables
merge_file_patterns	Character vector of file patterns to look for and merge to make the final output matrices

Details

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ import_model_data ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Benjamin-Vincent-Lab/binfotron documentation built on April 11, 2025, 10:05 p.m.