echoAI/README.Rmd at main · RajLabMSSM/echoAI · GitHub

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---
title: ""
author: "`r rworkflows::use_badges(branch = 'main', add_doi = '10.1093/bioinformatics/btab658')`"
output:
  github_document
---

```{r, echo=FALSE, include=FALSE}
pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
description <- read.dcf("DESCRIPTION", fields = "Description")[1] |>
    gsub(pattern="\n", replacement=" ")
```

## `r pkg`: `r gsub("echoverse module: ","", description, ignore.case = TRUE)`

This R package is part of the *echoverse* suite that supports
[`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR):
an automated genomic fine-mapping pipeline.

If you use `r pkg`, please cite:

> Brian M. Schilder, Jack Humphrey, Towfique Raj (2021) echolocatoR:
> an automated end-to-end statistical and functional genomic fine-mapping
> pipeline, *Bioinformatics*; btab658,
> https://doi.org/10.1093/bioinformatics/btab658

## Installation

```R
if(!require("BiocManager")) install.packages("BiocManager")

BiocManager::install("RajLabMSSM/echoAI")
library(echoAI)
```

## Functions

### Query & annotation

- `IMPACT_query()` : Query IMPACT annotations and LD-scores from
  tabix-indexed files on Zenodo. Supports wide, long, and list output formats.
- `IMPACT_get_annotations()` : Download raw IMPACT annotation matrices from
  GitHub and merge with your variant data.
- `IMPACT_get_annotation_key()` : Retrieve the IMPACT annotation key
  describing tissue, cell type, and transcription factor metadata for all
  707 annotations.

### Enrichment

- `IMPACT_compute_enrichment()` : Compute enrichment of IMPACT scores across
  SNP groups (lead GWAS, credible sets, consensus).
- `IMPACT_iterate_enrichment()` : Run enrichment tests across all loci.

### Visualisation

- `IMPACT_snp_group_boxplot()` : Box/violin plot of IMPACT scores by
  SNP group with statistical comparisons.
- `IMPACT_plot_enrichment()` : Bar and violin plots summarising enrichment
  results.
- `IMPACT_plot_impact_score()` : Multi-panel locus plot combining GWAS,
  fine-mapping, and per-tissue IMPACT scores.
- `IMPACT_heatmap()` : ComplexHeatmap of mean IMPACT scores across loci
  and SNP groups.

## Documentation

### [Website](https://rajlabmssm.github.io/`r pkg`)
### [Get started](https://rajlabmssm.github.io/`r pkg`/articles/`r pkg`)

<hr>

## Contact

<a href="https://bschilder.github.io/BMSchilder/" target="_blank">Brian
M. Schilder, Bioinformatician II</a>
<a href="https://rajlab.org" target="_blank">Raj Lab</a>
<a href="https://icahn.mssm.edu/about/departments-offices/neuroscience" target="_blank">Department
of Neuroscience, Icahn School of Medicine at Mount Sinai</a>