Targeted learning with the moderated t-statistic for biomarker discovery
biotmle is an R package that facilitates biomarker discovery by generalizing
the moderated t-statistic of Smyth for use with asymptotically linear target
parameters. The set of methods implemented in this R package rely on the use of
Targeted Minimum Loss-Based Estimation (TMLE) to transform biological sequencing
data (e.g., microarray, RNA-seq) based on the influence curve representation of
a particular statistical target parameter (e.g., the Average Treatment Effect).
The transformed data is then used to test for group differences using the
moderated t-statistic as implemented in the R package
limma.
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For standard use, install from Bioconductor:
source("https://bioconductor.org/biocLite.R") biocLite("biotmle")
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Install the most recent stable release from GitHub:
devtools::install_github("nhejazi/biotmle")
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To contribute, install the development version:
devtools::install_github("nhejazi/biotmle", ref = "develop")
If you encounter any bugs or have any specific feature requests, please file an issue.
After using the biotmle R package, please cite it:
@article{hejazi2017biotmle,
doi = {},
url = {},
year = {2017},
month = {},
publisher = {The Open Journal},
volume = {},
number = {},
author = {Hejazi, Nima S and Cai, Weixin and Hubbard, Alan E},
title = {biotmle: Targeted Learning for Biomarker Discovery},
journal = {The Journal of Open Source Software}
}
© 2016-2017 Nima S. Hejazi & Alan E. Hubbard
The contents of this repository are distributed under the MIT license. See file
LICENSE for details.