compute_np {crosstalkr}

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