-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.Rmd
45 lines (33 loc) · 2.62 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# WExT <a href="https://jhrcook.github.io/wext/"> <img src="man/figures/logo.png" align="right" alt="" width="120" /> </a>
<!-- badges: start -->
[](https://www.gnu.org/licenses/gpl-3.0)
[](https://cran.r-project.org/package=wext)
[](https://ci.appveyor.com/project/jhrcook/wext)
[](https://travis-ci.org/jhrcook/wext)
[](https://codecov.io/gh/jhrcook/wext?branch=master)
<!-- badges: end -->
The somatic mutations in the pathways that drive cancer development tend to be mutually exclusive across tumors, providing a signal for distinguishing driver mutations from a larger number of random passenger mutations. This mutual exclusivity signal can be confounded by high and highly variable mutation rates across a cohort of samples. Current statistical tests for exclusivity that incorporate both per-gene and per-sample mutational frequencies are computationally expensive and have limited precision.
WExT is a weighted exact test for assessing the significance of mutual exclusivity in an arbitrary number of mutational events. It conditions on the number of samples with a mutation as well as per-event, per-sample mutation probabilities. We provide a recursive formula to compute *P*-values for the weighted test exactly as well as a highly accurate and efficient saddle-point approximation of the test.
[The Weighted Exclusivity Test (WExT)](https://github.com/raphael-group/wext) was developed by the [Raphael research group](http://compbio.cs.brown.edu/) at Brown University and originally implemented as a command line tool running in Python. This is an adaptation for R with specific intention to be compatible with the ['tidyverse'](https://www.tidyverse.org).
## Installation
**This package is still in development and not ready for use.**
You can install the released version of wext from [CRAN](https://CRAN.R-project.org) with:
``` {r cran_install, eval=FALSE}
install.packages("wext")
```
or from GitHub using 'devtools':
```{r github_install, eval=FALSE}
devtools::install_github("jhrcook/wext")
```