README.Rmd

---
title: "README"
output: github_document
date: "2026-16-06"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# PEIMAN2 <a href='https://github.com/pnickchi/PEIMAN2/'><img src="vignettes/logo.png" align="right" height="139"/></a>

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[![CRAN status](https://www.r-pkg.org/badges/version/PEIMAN2)](https://cran.r-project.org/package=PEIMAN2) 
[![Github All Releases](https://cranlogs.r-pkg.org/badges/PEIMAN2)](https://github.com/pnickchi/PEIMAN2)

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The PEIMAN2 package @PEIMAN2 provides functions and mined database from UniProt for single enrichment analysis (SEA) and protein set enrichment analysis (PSEA) in a list of protein. The database is updated regularly with monthly changes in UniProt/SwissProt repository. To ensure you have the latest version of database, make sure to install the package from GitHub. 


## Installation

You can install the released version of PEIMAN from [CRAN](https://CRAN.R-project.org) with:

```{r, eval=FALSE}
install.packages("PEIMAN2")
```


And the development version from [GitHub](https://github.com/) with:

```{r, eval=FALSE}
# install.packages("devtools")
devtools::install_github("jafarilab/PEIMAN2")
# or
devtools::install_github("pnickchi/PEIMAN2")
```


## Example

### Singular Enrichment Analysis (SEA)

```{r}
# Load PEIMAN2 package
library(PEIMAN2)

# First example dataset
pl1 <- exmplData1$pl1

# Run SEA on the list
enrich1 <- runEnrichment(protein = pl1, os.name = 'Homo sapiens (Human)')

head(enrich1, n = 6)
```


```{r}
# Second example dataset
pl2 <- exmplData1$pl2

# Run SEA on the list
enrich2 <- runEnrichment(protein = pl2, os.name = 'Homo sapiens (Human)')
```


### Plotting SEA for one list

```{r}
plotEnrichment(x = enrich1, sig.level = 0.05)
```


### Integration and matching analysis of two lists

```{r}
plotEnrichment(x = enrich1, y = enrich2, sig.level = 0.05)
```


### Protein Set Enrichment Analysis (PSEA)

```{r}
psea_res <- runPSEA(protein = exmplData2, os.name = 'Rattus norvegicus (Rat)', nperm = 100)
head(psea_res[[1]], n = 6)
```

### Plotting PSEA

```{r, fig.width=14, fig.height=12, fig.align='center'}
plotPSEA(x = psea_res)
```


```{r}
plotRunningScore(x = psea_res, nplot = 8) 
```


### Translate PEIMAN results for Mass spectrometry searching tools

```{r}
psea2mass(x = psea_res, sig.level = 0.05)
```