compute_dnp {crosstalkr}

main function to compute delta np for every gene in a given dataframe - assumes compute_np has already been run for a given dataset

Description

This function takes a tidy dataframe as input containing RNA sequencing data for one or more samples and conducts in-silico repression. Make sure to run with the same arguments for ppi and cache to maintain consistency for a given pipeline.

Usage

compute_dnp(
  cache = NULL,
  df,
  experiment_name,
  ppi,
  ncores = 1,
  min_score = NULL
)

Arguments

cache

user-provided filepath for where to store data etc

df

dataframe output of compute_np

experiment_name

name of the experiment for saving output.

ppi

should we use biogrid or stringdb for the PPI

ncores

number of cores to use for calculations

min_score

if ppi is stringdb, which mininum score should we use to filter edges?

Value

data.frame