compute_dnp: main function to compute delta np for every gene in a given...

In DavisWeaver/disruptr: Facilitate in-silico repression experiments on graph-structured data

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?

DavisWeaver/disruptr documentation built on Jan. 29, 2023, 1:04 a.m.