forked from wilsoncai1992/adaptest
-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathREADME.Rmd
More file actions
153 lines (112 loc) · 5.64 KB
/
Copy pathREADME.Rmd
File metadata and controls
153 lines (112 loc) · 5.64 KB
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
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
---
output: rmarkdown::github_document
bibliography: "README-refs.bib"
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# R/`adaptest`
[](https://travis-ci.org/wilsoncai1992/adaptest?branch=master)
[](https://ci.appveyor.com/project/wilsoncai1992/adaptest/)
[](https://codecov.io/github/wilsoncai1992/adaptest?branch=master)
[](https://www.repostatus.org/#active)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/adaptest)
[](https://bioconductor.org/packages/release/bioc/html/adaptest.html)
[](https://bioconductor.org/packages/release/bioc/html/adaptest.html)
[](http://www.gnu.org/licenses/gpl-2.0.html)
[](https://doi.org/10.5281/zenodo.1466019)
[](https://doi.org/10.21105/joss.00161)
> Data-adaptive statistics for multiple testing in high-dimensional biology
__Authors:__ [Wilson Cai](https://stat.berkeley.edu/~wcai) and [Nima
Hejazi](https://nimahejazi.org)
---
## What's `adaptest`?
The `adaptest` R package is a tool for performing multiple testing on effect
sizes in high-dimensional settings, using the approach of data-adaptive
statistical target parameters and inference. For technical details on the
data-adaptive multiple testing procedure, consult @cai2018data. For an
introduction to statistical inference procedures using data-adaptive target
parameters, the interested reader is directed to @hubbard2016statistical.
---
## Installation
For standard use, install from
[Bioconductor](https://bioconductor.org/packages/adaptest) using
[`BiocManager`](https://CRAN.R-project.org/package=BiocManager):
```{r bioc-installation, eval = FALSE}
if (!requireNamespace("BiocManager", quietly=TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("adaptest")
```
To contribute, install the _development version_ (i.e., branch __`master`__)
from GitHub via
[`devtools`](https://www.rstudio.com/products/rpackages/devtools/):
```{r gh-master-installation, eval = FALSE}
devtools::install_github("wilsoncai1992/adaptest")
```
Current and prior [Bioconductor](https://bioconductor.org) releases are
available under branches with numbers prefixed by "RELEASE_". For example, to
install the version of this package available via Bioconductor 3.7, use
```{r gh-develop-installation, eval = FALSE}
devtools::install_github("wilsoncai1992/adaptest", ref = "RELEASE_3_7")
```
**_Note_: As the first stable release of this package was through Bioconductor
v3.7, the minimum version of [R](https://www.r-project.org/) required to
install `adaptest` is 3.5.0 (codename "Joy in Playing").**
---
## Example
For details on how to best use the `adaptest` R package, please consult the most
recent [package
vignette](https://bioconductor.org/packages/release/bioc/vignettes/adaptest/inst/doc/differentialExpression.html)
available through the [Bioconductor
project](https://bioconductor.org/packages/adaptest).
---
## Issues
If you encounter any bugs or have any specific feature requests, please [file an
issue](https://github.com/wilsoncai1992/adaptest/issues).
---
## Contributions
Contributions are very welcome. Interested contributors should consult our
[contribution
guidelines](https://github.com/wilsoncai1992/adaptest/blob/master/CONTRIBUTING.md)
prior to submitting a pull request.
---
## Citation
After using the `adaptest` R package, please cite the following
@article{cai2018adaptest,
doi = {10.21105/joss.00161},
url = {https://doi.org/10.21105/joss.00161},
year = {2018},
month = {October},
publisher = {The Open Journal},
volume = {3},
number = {30},
author = {Cai, Weixin and Hubbard, Alan E and Hejazi, Nima S},
title = {{adaptest}: Data-Adaptive Statistics for High-Dimensional
Testing in {R}},
journal = {The Journal of Open Source Software}
}
@article{cai2018+adaptive,
url = {https://arxiv.org/abs/1704.07008},
year = {2018+},
author = {Cai, Weixin and Hejazi, Nima S and Hubbard, Alan E},
title = {Data-adaptive statistics for multiple hypothesis testing in
high-dimensional settings}
}
---
## Funding
The development of this software was supported in part through grants from the
National Institutes of Health: [P42 ES004705-29](https://projectreporter.nih.gov/project_info_details.cfm?aid=9260357&map=y)
and [T32 LM012417-02](https://projectreporter.nih.gov/project_info_description.cfm?aid=9248418&icde=37849831&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=).
---
## License
© 2017-2018 [Wilson Cai](https://statistics.berkeley.edu/~wcai)
The software contents of this repository are distributed under the GPL-2
license. See file `LICENSE` for details.
---
## References