define_plan: Initialize and return drake_plan object. New for github drake...

In brandonsie/phipmake: PhIP-seq Data Analysis Pipeline

Initialize and return drake_plan object. New for github drake 7.0+.

Description

Initialize and return drake_plan object. New for github drake 7.0+.

Usage

define_plan(
  params_path = "drake_params.tsv",
  runCounts = TRUE,
  runPairwise = FALSE,
  runFoldChange = TRUE,
  runEnrichment = TRUE,
  runHits = TRUE,
  runPolyclonal = TRUE,
  runAVARDA = FALSE,
  runEpitopefindr = FALSE,
  runEpitopefindr_nolatex = FALSE
)

Arguments

params_path	Path to project parameters file that can be created using the write_drake_params function.
runCounts	Logical controlling whether or not to define counts targets.
runPairwise	Logical controlling whether or not to define pairwise targets.
runFoldChange	Logical controlling whether or not to define EdgeR fold change targets.
runEnrichment	Logical controlling whether or not to define enrichment targets.
runPolyclonal	Logical controlling whether or not to define enrichment targets.
runAVARDA	Logical controlling whether or not to define AVARDA targets.
runEpitopefindr	Logical controlling whether or not to run epitopefindr analysis on hits.
runEpitopefindr_nolatex	Logical controlling whether or not to run epitopefindr analysis on hits without latex (replaces epitopefindr_latex).
epitopefindr_latex	(no longer used) Logical controlling whether to generate LaTeX from epitopefindr multiple sequence alignments.

brandonsie/phipmake documentation built on March 15, 2023, 3:24 p.m.