compute_np: main function to compute np from a user-provided expression...

In crosstalkr: Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks

main function to compute np from a user-provided expression matrix.

Description

main function to compute np from a user-provided expression matrix.

Usage

compute_np(
  cache = NULL,
  experiment_name,
  ppi = "biogrid",
  min_score = NULL,
  exp_mat,
  mir_paper = TRUE,
  ncores = 1
)

Arguments

cache	user-provided filepath for where to store data etc
experiment_name	name of the experiment for saving output.
ppi	should we use biogrid or stringdb for the PPI
min_score	if ppi is stringdb, which mininum score should we use to filter edges?
exp_mat	expression matrix where columns are samples and rows are features
mir_paper	are we running this in the context of the mir paper? a few quirks of that data
ncores	number of cores to use for calculations

Value

tidy data frame with one column for expression and another for np

crosstalkr documentation built on Sept. 30, 2023, 1:06 a.m.