README.md

In Waller-SUSAN/gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

gateR: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

Date repository last updated: January 23, 2024

Overview

The gateR package is a suite of R functions to identify significant spatial clustering of flow and mass cytometry data used in immunological investigations. For a two-group comparison, we detect clusters using the kernel-based spatial relative risk function estimated using the sparr package. The tests are conducted in a two-dimensional space comprised of two fluorescent markers.

Examples of a single condition with two groups:

1. Disease case vs. Healthy control
2. Time 2 vs. Time 1 (baseline)

For a two-group comparison of two conditions, we estimate two relative risk surfaces for one condition and then a ratio of the relative risks. For example:

1. Estimate a relative risk surface for:
   1. Condition 2B vs. Condition 2A
   2. Condition 1B vs. Condition 1A
2. Estimate the relative risk surface for the ratio:

$$\frac{ \big(\frac{Condition2B}{Condition2A}\big)}{\big(\frac{Condition1B}{Condition1A}\big)}$$

Within areas where the relative risk exceeds an asymptotic normal assumption, the gateR package has the functionality to examine the features of these cells. Basic visualization is also supported.

Installation

To install the release version from CRAN:

install.packages("gateR")

To install the development version from GitHub:

devtools::install_github("lance-waller-lab/gateR")

Available functions

Function Description gating Main function. Conduct a gating strategy for flow and mass cytometry data. rrs Called within gating, one condition comparison. lotrrs Called within gating, two condition comparison. pval_correct Called within rrs and lotrrs, calculates various multiple testing corrections for the alpha level. Five methods account for (spatially) dependent, multiple testing. lrr_plot Called within rrs and lotrrs, provides functionality for basic visualization of a log relative risk surface. pval_plot Called within rrs and lotrrs, provides functionality for basic visualization of a significant p-value surface. The repository also includes the code and resources to create the project hexagon sticker.

Available sample data sets

Data Description randCyto A sample dataset containing information about flow cytometry data with two binary conditions and four markers. The data are a random subset of the 'extdata' data in the flowWorkspaceData package found on Bioconductor and formatted for `gateR` input.

Authors

* **Ian D. Buller** - *Social & Scientific Systems, Inc., a division of DLH Corporation, Silver Spring, Maryland (current)* - *Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland (former)* - *Environmental Health Sciences, James T. Laney School of Graduate Studies, Emory University, Atlanta, Georgia. (original)* - [GitHub](https://github.com/idblr) - [ORCID](https://orcid.org/0000-0001-9477-8582) See also the list of [contributors](https://github.com/lance-waller-lab/gateR/graphs/contributors) who participated in this project. Main contributors include: * **Elena Hsieh** - *Immunology & Microbiology and Pediatrics, University of Colorado Anschutz School of Medicine* - [GitHub](https://github.com/elenahsieh1407) - [ORCID](https://orcid.org/0000-0003-3969-6597) * **Debashis Ghosh** - *Biostatistics & Informatics, Colorado School of Public Health, Aurora, Colorado* - [GitHub](https://github.com/ghoshd) - [ORCID](https://orcid.org/0000-0001-5672-7645) * **Lance A. Waller** - *Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia* - [GitHub](https://github.com/lance-waller) - [ORCID](https://orcid.org/0000-0001-5002-8886) ## Usage wzxhzdk:0    wzxhzdk:1 ### Funding This package was developed while the author was originally a doctoral student at in the [Environmental Health Sciences doctoral program](https://sph.emory.edu/departments/eh/degree-programs/phd/index.html) at [Emory University](https://www.emory.edu/home/index.html) and later as a postdoctoral fellow supported by the [Cancer Prevention Fellowship Program](https://cpfp.cancer.gov/) at the [National Cancer Institute](https://www.cancer.gov/). Any modifications since December 05, 2022 were made while the author was an employee of Social & Scientific Systems, Inc., a division of [DLH Corporation](https://www.dlhcorp.com). ### Acknowledgments When citing this package for publication, please follow: citation("gateR") ### Questions? Feedback? For questions about the package, please contact the maintainer [Dr. Ian D. Buller](mailto:[e-mail]) or [submit a new issue](https://github.com/lance-waller-lab/gateR/issues).

Waller-SUSAN/gateR documentation built on Feb. 5, 2024, 12:54 p.m.