README.md

In rachaelcox/enrichr: Compute Protein Enrichment

enrichr

Annotate, compute, and visualize fold-changes and Z-scores for differential proteomics results.

Functions

enrich(): Compute AUC XICs fold-changes (optional) and PSMs fold-changes/Z-scores for _Proteins.txt and _PSMs.txt assignment files output by Proteome Discoverer 2.3. Annotates results given an annotation table (optional). Annotation table must contain column with name ending in gene_names_primary.

psmplot(): Visualize control PSMs versus test PSMs on a log-log plot. Uses dataframe output by enrich() as input. Requires annotation column with name ending in gene_names_primary.

combine_reps(): Combine biological replicates, i.e., combines dataframes output by enrich().

combine_exps(): Combines experiments, i.e., combines dataframes output by combine_reps().

zplot(): Visualize PSM-based Z-scores for proteins biological replicates. Uses dataframe output by combine_reps() or combine_exps() as input. Requires annotation column with name ending in gene_names_primary.

Installation

Run the following code:

install.packages("devtools")  # if devtools not installed
devtools::install_github("rachaelcox/enrichr")
library(enrichr)

Example workflow

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