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

In DavisWeaver/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

DavisWeaver/crosstalkr documentation built on May 6, 2024, 6:09 p.m.