parameter_grid: Implement pipeline workflow over a grid of parameters.

Description Usage Arguments Value

View source: R/parameter_grid.R

Description

Given a dataframe of differential gene expression results, this function will implement the specified pipeline with each combination of parameters and return a dataframe of performance evaluation metrics.

Usage

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parameter_grid(
  deg,
  target,
  grid,
  pipeline_method = NULL,
  connected_filter = NULL,
  n_cores = 1,
  ...
)

Arguments

deg

Object of class 'dataframe'. Differential gene expression analysis results including log fold-changes and p-values, i.e. the output of topTable() from limma or results() from DESeq2.

target

A string. The gene symbol associated with the causal gene.

grid

Object of class 'dataframe', where each row corresponds to a combination of parameter values. i.e. the output of expand.grid().

n_cores

Numeric. Number of cores to run on. Default value is 1.

pipeline

String. The workflow pipeline to be used. The value can be either 'centrality' or 'propagation', corresponding the centrality_pipeline() and propagation_pipeline() functions.

method

A string specifying the network analysis method for the pipeline. See ?centrality_pipeline() or ?propagation_pipeline() for more.

Value

Object of class 'dataframe', with columns corresponding to the parameter combination implemented and the


taylorpourtaheri/nr documentation built on Dec. 23, 2021, 7:49 a.m.