gpwm/README.Rmd at master · tanaylab/gpwm · GitHub

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---
output: github_document
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  eval = FALSE
)
```
# gpwm

<!-- badges: start -->
<!-- badges: end -->

The goal of gpwm is to supply functions for analysis of PWM motifs using the misha package.

## Installation

You can install gpwm by running:

```r
remotes::install_github("aviezerl/gpwm")
```

## Example
```r
library(gpwm)
library(tidyverse)

# Set misha database
gsetroot("/net/mraid14/export/data/db/tgdb/mm9/trackdb/")

# Define foreground intervals
intervals_fg <- get_promoters(upstream = 40, downstream=10) %>% sample_n(1e4)

# Define background intervals
intervals_bg <- get_promoters(upstream = 40, downstream=10) %>% anti_join(intervals_fg)


intervals <- bind_rows(
	intervals_fg %>% mutate(type = 'fg'),
	intervals_bg %>% mutate(type = 'bg')
)

# Extract motifs
motifs <- gpwm.extract_all('motifs_10bp', intervals)

# Calculate enrichment
enrich <- gpwm.motif_enrich(
	fg = motifs %>% filter(type == "fg"),
	bg = motifs %>% filter(type == "bg"),
	pattern = "motifs_10bp",
	size = 50,
	quantile_thresh=0.99,
	max.jobs = 5)
```