# leapR
Layered Enrichment Analysis of Pathways in R (leapR) a tool that carries out statistical enrichment analysis on single- or multi-omics data.
## Install
leapR is available through Bioconductor repository here
```{r install}
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.21")
BiocManager::install('BiocStyle')
BiocManager::install('leapR')
```
Once you have successfully installed the package you can load the vignette to read examples using the `vignette('leapR')` command.
## Basic Usage
The primary function of the `leapR` package is the `leapR` function itself. This function serves a wrapper to run different styles of enrichment functions on the data. The package contains other functions to support pathway information and multi-omics datasets.
### Enrichment calls
Here is a list of enrichment arguments that can be called with the `leapR` command.
| Argument | Description |
| --- | ---- |
| `enrichment_in_sets` | Calculates enrichment in pathway membership in a list (e.g. highly differential proteins) relative to background using Fisher's exact test. |
| `enrichment_in_order` | Calculates enrichment of pathways based on a ranked list using the Kolmogorov-Smirnov test |
| `enrichment_comparison` | Compares the distribution of abundances between two sets of conditions for each pathway using a t test |
| `enrichment_in_pathways` | Compares the distribution of abundances in a pathway with the background distribution of abundances using a t test |
|`correlation_enrichment` | Calculates the enrichment of a pathway based on correlation between pathway members across conditions versus correlation between members not in the pathway |
| `enrichment_in_relationships`| Calculates the enrichment of a pathway in specified interactions relative to non-pathway members |
### Data examples
We included examples of including proteomics data and transcriptomics data from 169 high-grade serous ovarian cancer (HGSOC) tumors previously studied and lists of the short- and long- surviving patients from that cohort.
### Gene pathway examples
We included two different gene pathways. An NCI pathway database (Pathway Information Database; PID) of signaling pathways and the MSIGDB set of gene collections from various sources.
