write_drake_params: write_drake_params

In brandonsie/phipmake: PhIP-seq Data Analysis Pipeline

write_drake_params

Description

write default values to drake_params.tsv for phipmake pipeline

Usage

write_drake_params(
  dir,
  screen_name,
  counts_filename = "counts.csv",
  counts_type = "Counts",
  foldchange_filename = "fold_change.csv",
  foldchange_type = "FoldChange",
  enrichment_filename = "enrichment.csv",
  enrichment_type = "Enrichment",
  hits_filename = "Hits.csv",
  metadata_path = "/data/hlarman1/PhIPdb/Metadata/PeptideLibraries",
  output_extension = "tsv"
)

Arguments

dir	PhIP-seq project directory.
screen_name	Identifier for multiplexed screen, e.g. phipseq_0001.
counts_filename	Name of demultiplexed, merged reads file in screen directory.
counts_type	Identifier for type of counts data to append in output file names.
foldchange_filename	Name of demultiplexed, merged foldchange file in screen directory.
foldchange_type	Identifier for type of counts data to append in output file names.
enrichment_filename	Name of demultiplexed, merged enrichment file in screen directory.
enrichment_type	Identifier for type of enrichment data to append in output file names.
hits_filename	Name of demultiplexed, merged hits file in screen directory.
metadata_path	Directory path string to metadata folder containing peptide files and intrapeptide blast alignment files.
output_extension	Extension for tab-separated output files.

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