combine_reps: Combine replicates for a proteomics experiment.

In rachaelcox/enrichr: Compute Protein Enrichment

Description

Combine replicate proteomics experiments. Calculates mean PSMs across test and control runs. Calculates weighted z-scores using Stouffer's Z-score method. Calculates p-values and FDR on the weighted Z-score using the Benjamini-Hochberg procedure. See README for file formats and example usage on the enrichr GitHub Repository.

Usage

combine_reps(rep1, rep2, rep3, one_sided = FALSE, outfile_prefix)

Arguments

rep1	A data frame produced by enrich_fxn() corresponding to replicate 1.
rep2	A data frame produced by enrich_fxn() corresponding to replicate 2.
rep3	Optional. A data frame produced by enrich_fxn() corresponding to replicate 3.
one_sided	Specify one-sided or two-sided statistical test; default = FALSE (two-sided).
outfile_prefix	Optional. File prefix for output .csv files. Default = "reps_combined".

Value

A data frame and .csv with PSM information across biological replicates combined into one table.

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