enrich: Annotate and compute fold-changes and Z-scores for...

In rachaelcox/enrichr: Compute Protein Enrichment

Description

Format PSM.txt and Proteins.txt files output by Proteome Discoverer 2.3, formatting PSM counts and AUC XIC values into one table, summing technical replicates, and computing fold-change and Z-scores for each detected protein in test and control runs. Optionally annotates results given a tab-separated annotation file. See README for file formats and example usage on the enrichr GitHub Repository.

Usage

enrich(
  exp_id,
  meta_file,
  psm_file,
  pd_file,
  one_sided = FALSE,
  annot_file,
  outfile_name = "output.csv"
)

Arguments

exp_id	An identifier for a given experiment that matches test and control files together (see meta file).
meta_file	A tab-separate file with column headers exp_name (populated with values that correspond to exp_id variable), type (exp or ctrl), and file_id (determined by Proteome Discoverer, see README on Github).
psm_file	PSM.txt tab-separated file output by Proteome Discoverer 2.3.
pd_file	Proteins.txt tab-separated file output by Proteome Discoverer 2.3.
one_sided	Specify one-sided or two-sided statistical test; default = FALSE (two-sided).
annot_file	Optional tab-separated file containing a table with annotations for the queried proteome; must match accession format in FASTA given to Proteome Discoverer as a look up database.
outfile_name	File name for output .csv; default = "output.csv".

Value

A .csv with all computed information combined into one table.

rachaelcox/enrichr documentation built on Jan. 19, 2021, 2:11 p.m.