Data

Tools

Indexes

Applications

Experiments

Open Source Science

qtl2pleio

qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations - Published in JOSS (2019)

https://github.com/fboehm/qtl2pleio

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

multiparental-populations quantitative-genetics quantitative-trait

Scientific Fields

Engineering Computer Science - 60% confidence
Last synced: 6 months ago · JSON representation

Repository

Testing pleiotropy vs. separate QTL in multiparental populations

Basic Info
  • Host: GitHub
  • Owner: fboehm
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 5.23 MB
Statistics
  • Stars: 5
  • Watchers: 2
  • Forks: 1
  • Open Issues: 11
  • Releases: 9
Topics
multiparental-populations quantitative-genetics quantitative-trait
Created over 8 years ago · Last pushed over 4 years ago
Metadata Files
Readme Changelog License Codemeta Zenodo

README.Rmd 

---
output: github_document
---





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

# qtl2pleio

[![R-CMD-check](https://github.com/fboehm/qtl2pleio/workflows/R-CMD-check/badge.svg)](https://github.com/fboehm/qtl2pleio/actions)
[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/qtl2pleio)](https://cran.r-project.org/package=qtl2pleio)
[![Coverage Status](https://img.shields.io/codecov/c/github/fboehm/qtl2pleio/master.svg)](https://codecov.io/github/fboehm/qtl2pleio?branch=master)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![status](https://joss.theoj.org/papers/66bca5dc3d2e72b6259159bad07aafaf/status.svg)](https://joss.theoj.org/papers/10.21105/joss.01435)
[![DOI](https://zenodo.org/badge/104493705.svg)](https://zenodo.org/badge/latestdoi/104493705)




## Overview

`qtl2pleio` is a software package for use with the [R statistical computing environment](https://cran.r-project.org/). `qtl2pleio` is freely available for download and use. I share it under the [MIT license](https://opensource.org/licenses/mit-license.php). The user will also want to download and install the [`qtl2` R package](https://kbroman.org/qtl2/).

Click [here](https://mybinder.org/v2/gh/fboehm/qtl2pleio/master?urlpath=rstudio) to explore `qtl2pleio` within a live [Rstudio](https://rstudio.com/) session in "the cloud".

## Contributor guidelines

We eagerly welcome contributions to `qtl2pleio`. All pull requests will be considered. Features requests and bug reports may be filed as Github issues. All contributors must abide by the [code of conduct](https://github.com/fboehm/qtl2pleio/blob/master/CONDUCT.md). 

## Technical support 

For technical support, please open a Github issue. If you're just getting started with `qtl2pleio`, please examine the [vignettes](https://fboehm.us/software/qtl2pleio) on the [package's web site](https://fboehm.us/software/qtl2pleio). You can also email  for assistance. 




## Goals

The goal of `qtl2pleio` is, for a pair of traits that show evidence for
a QTL in a common region, to distinguish between pleiotropy (the null
hypothesis, that they are affected by a common QTL) and the
alternative that they are affected by separate QTL. It extends the
likelihood ratio test of [Jiang and Zeng
(1995)](https://www.genetics.org/content/140/3/1111.long) for
multiparental populations, such as Diversity Outbred mice, including
the use of multivariate polygenic random effects to account for population structure.
`qtl2pleio` data structures are those used in the
[`rqtl/qtl2`](https://kbroman.org/qtl2/) package.


## Installation


To install qtl2pleio, use `install_github()` from the
[devtools](https://devtools.r-lib.org) package.


```{r install-qtl2pleio, eval = FALSE}
install.packages("qtl2pleio")
```

You may also wish to install the [R/qtl2](https://kbroman.org/qtl2/). We
will use it below.

```{r install-qtl2, eval = FALSE}
install.packages("qtl2")
```


## Example

Below, we walk through an example analysis with Diversity Outbred
mouse data. We need a number of preliminary steps before we can
perform our test of pleiotropy vs. separate QTL. Many procedures rely
on the R package `qtl2`. We first load the `qtl2`
and `qtl2pleio` packages.

```{r pkgs}
library(qtl2)
library(qtl2pleio)
library(ggplot2)
```


### Reading data from `qtl2data` repository on github

We'll consider the
[`DOex`](https://github.com/rqtl/qtl2data/tree/master/DOex/) data in
the [`qtl2data`](https://github.com/rqtl/qtl2data/) repository.
We'll download the DOex.zip file before calculating founder allele dosages.

```{r download-DOex}
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/master/DOex/DOex.zip")
DOex <- read_cross2(file)
```


```{r calc-genoprobs}
probs <- calc_genoprob(DOex)
```


Let's calculate the founder allele dosages from the 36-state genotype probabilities.

```{r calc-allele-probs}
pr <- genoprob_to_alleleprob(probs)
```


We now have an allele probabilities object stored in `pr`.

```{r check-pr}
names(pr)
dim(pr$`2`)
```

We see that `pr` is a list of 3 three-dimensional arrays - one array for each of 3 chromosomes.

### Kinship calculations

For our statistical model, we need a kinship matrix. We get one with the `calc_kinship` function in the `rqtl/qtl2` package.


```{r calc-kinship}
kinship <- calc_kinship(probs = pr, type = "loco")
```

### Statistical model specification

We use the multivariate linear mixed effects model:

$$
\text{vec}(Y) = X \text{vec}(B) + \text{vec}(G) + \text{vec}(E)
$$

where $Y$ contains phenotypes, X contains founder allele probabilities and covariates, and B contains founder allele effects. G is the polygenic random effects, while E is the random errors. We provide more details in the vignette.



### Simulating phenotypes with `qtl2pleio::sim1`


The function to simulate phenotypes in `qtl2pleio` is `sim1`.

```{r pp-def}
# set up the design matrix, X
pp <- pr[[2]] #we'll work with Chr 3's genotype data
```


```{r X-def}
#Next, we prepare a design matrix X
X <- gemma2::stagger_mats(pp[ , , 50], pp[ , , 50])
```

```{r B-def}
# assemble B matrix of allele effects
B <- matrix(data = c(-1, -1, -1, -1, 1, 1, 1, 1, -1, -1, -1, -1, 1, 1, 1, 1), nrow = 8, ncol = 2, byrow = FALSE)
# set.seed to ensure reproducibility
set.seed(2018-01-30)
Sig <- calc_Sigma(Vg = diag(2), Ve = diag(2), kinship = kinship[[2]])
# call to sim1
Ypre <- sim1(X = X, B = B, Sigma = Sig)
Y <- matrix(Ypre, nrow = 261, ncol = 2, byrow = FALSE)
rownames(Y) <- rownames(pp)
colnames(Y) <- c("tr1", "tr2")
```

Let's perform univariate QTL mapping for each of the two traits in the Y matrix.

```{r 1d-scans}
s1 <- scan1(genoprobs = pr, pheno = Y, kinship = kinship)
```

Here is a plot of the results.

```{r 1d-lod-plots, include=FALSE}
plot(s1, DOex$pmap)
plot(s1, DOex$pmap, lod=2, col="violetred", add=TRUE)
legend("topleft", colnames(s1), lwd=2, col=c("darkslateblue", "violetred"), bg="gray92")
```

```{r, echo = FALSE}
knitr::include_graphics("https://raw.githubusercontent.com/fboehm/qtl2pleio/master/man/figures/README-1d-lod-plots-1.png")
```

And here are the observed QTL peaks with LOD > 8.

```{r find-peaks}
find_peaks(s1, map = DOex$pmap, threshold=8)
```





### Perform two-dimensional scan as first step in pleiotropy vs. separate QTL hypothesis test


We now have the inputs that we need to do a pleiotropy vs. separate QTL test. We have the founder allele dosages for one chromosome, *i.e.*, Chr 3, in the R object `pp`, the matrix of two trait measurements in `Y`, and a LOCO-derived kinship matrix, `kinship[[2]]`.


```{r 2d-scan}
out <- suppressMessages(scan_pvl(probs = pp,
                pheno = Y,
                kinship = kinship[[2]], # 2nd entry in kinship list is Chr 3
                start_snp = 38,
                n_snp = 25
                ))
```


### Create a profile LOD plot to visualize results of two-dimensional scan

To visualize results from our two-dimensional scan, we calculate profile LOD for each trait. The code below makes use of the R package `ggplot2` to plot profile LODs over the scan region.


```{r profile-plot, include = TRUE}
library(dplyr)
out %>%
  calc_profile_lods() %>%
  add_pmap(pmap = DOex$pmap$`3`) %>%
  ggplot() + geom_line(aes(x = marker_position, y = profile_lod, colour = trait))
```




### Calculate the likelihood ratio test statistic for pleiotropy v separate QTL

We use the function `calc_lrt_tib` to calculate the likelihood ratio test statistic value for the specified traits and specified genomic region.

```{r lrt-calc}
(lrt <- calc_lrt_tib(out))
```

### Bootstrap analysis to get p-values


Before we call `boot_pvl`, we need to identify the index (on the chromosome under study) of the marker that maximizes the likelihood under the pleiotropy constraint. To do this, we use the `qtl2pleio` function `find_pleio_peak_tib`.

```{r get-pleio-index}
(pleio_index <- find_pleio_peak_tib(out, start_snp = 38))
```



```{r boot}
set.seed(2018-11-25) # set for reproducibility purposes.
b_out <- suppressMessages(boot_pvl(probs = pp,
         pheno = Y,
         pleio_peak_index = pleio_index,
         kinship = kinship[[2]], # 2nd element in kinship list is Chr 3
         nboot = 10,
         start_snp = 38,
         n_snp = 25
         ))
```


```{r pval}
(pvalue <- mean(b_out >= lrt))
```



## Citation information

```{r cite}
citation("qtl2pleio")
```

Owner

  • Name: Frederick Boehm
  • Login: fboehm
  • Kind: user
  • Location: Ann Arbor, Michigan, USA
  • Company: University of Michigan

I study biostatistics, with a focus in statistical genetics. I strive to understand how our genes influence our health and biology.

JOSS Publication

qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations
Published
June 30, 2019
DOI
Volume 4, Issue 38, Page 1435
Authors
Frederick Boehm ORCID
Department of Statistics, University of Wisconsin-Madison
Brian Yandell ORCID
Department of Statistics, University of Wisconsin-Madison
Karl W. Broman ORCID
Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison
Editor
Charlotte Soneson ORCID
Tags
qtl2 genetics systems genetics multiparental populations
View PDF Review Thread Software Archive

CodeMeta (codemeta.json) 

{
  "@context": [
    "https://doi.org/10.5063/schema/codemeta-2.0",
    "http://schema.org"
  ],
  "@type": "SoftwareSourceCode",
  "identifier": "qtl2pleio",
  "description": "We implement an\n    adaptation of Jiang & Zeng's (1995) <https://www.genetics.org/content/140/3/1111> likelihood ratio test for testing\n    the null hypothesis of pleiotropy against the alternative hypothesis,\n    two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) <https://www.genetics.org/content/140/3/1111> \n    and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in\n    that our test accommodates multiparental populations.",
  "name": "qtl2pleio: Testing Pleiotropy in Multiparental Populations",
  "codeRepository": "https://github.com/fboehm/qtl2pleio",
  "issueTracker": "https://github.com/fboehm/qtl2pleio/issues",
  "license": "https://spdx.org/licenses/MIT",
  "version": "1.4.3",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.0.3 (2020-10-10)",
  "author": [
    {
      "@type": "Person",
      "givenName": "Frederick J",
      "familyName": "Boehm",
      "email": "frederick.boehm@gmail.com",
      "@id": "https://orcid.org/0000-0002-1644-5931"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Frederick J",
      "familyName": "Boehm",
      "email": "frederick.boehm@gmail.com",
      "@id": "https://orcid.org/0000-0002-1644-5931"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "covr",
      "name": "covr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=covr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "mvtnorm",
      "name": "mvtnorm",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=mvtnorm"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "broman",
      "name": "broman",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=broman"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "devtools",
      "name": "devtools",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=devtools"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "qtl2",
      "name": "qtl2",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=qtl2"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "parallelly",
      "name": "parallelly",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=parallelly"
    }
  ],
  "softwareRequirements": [
    {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 3.2"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "dplyr",
      "name": "dplyr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=dplyr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "gemma2",
      "name": "gemma2",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=gemma2"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "ggplot2",
      "name": "ggplot2",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=ggplot2"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "magrittr",
      "name": "magrittr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=magrittr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "MASS",
      "name": "MASS",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=MASS"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "Rcpp",
      "name": "Rcpp",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=Rcpp"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rlang",
      "name": "rlang",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rlang"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "tibble",
      "name": "tibble",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tibble"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "parallel",
      "name": "parallel"
    }
  ],
  "releaseNotes": "https://github.com/fboehm/qtl2pleio/blob/master/NEWS.md",
  "readme": "https://github.com/fboehm/qtl2pleio/blob/master/README.md",
  "contIntegration": [
    "https://travis-ci.org/fboehm/qtl2pleio",
    "https://codecov.io/github/fboehm/qtl2pleio?branch=master"
  ],
  "keywords": [
    "quantitative-trait",
    "quantitative-genetics",
    "multiparental-populations"
  ],
  "contributor": {},
  "copyrightHolder": {},
  "funder": {},
  "developmentStatus": "https://www.repostatus.org/#active",
  "citation": [
    {
      "@type": "ScholarlyArticle",
      "datePublished": "2019",
      "author": [
        {
          "@type": "Person",
          "givenName": [
            "Frederick",
            "J."
          ],
          "familyName": "Boehm"
        },
        {
          "@type": "Person",
          "givenName": [
            "Elissa",
            "J."
          ],
          "familyName": "Chesler"
        },
        {
          "@type": "Person",
          "givenName": [
            "Brian",
            "S."
          ],
          "familyName": "Yandell"
        },
        {
          "@type": "Person",
          "givenName": [
            "Karl",
            "W."
          ],
          "familyName": "Broman"
        }
      ],
      "name": "Testing pleiotropy vs. separate QTL in multiparental populations",
      "url": "https://www.g3journal.org/content/9/7/2317",
      "isPartOf": {
        "@type": "PublicationIssue",
        "datePublished": "2019",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "volumeNumber": "9",
          "name": "G3"
        }
      }
    }
  ],
  "provider": {
    "@id": "https://cran.r-project.org",
    "@type": "Organization",
    "name": "Comprehensive R Archive Network (CRAN)",
    "url": "https://cran.r-project.org"
  },
  "fileSize": "66291.722KB",
  "relatedLink": "https://CRAN.R-project.org/package=qtl2pleio"
}

Papers & Mentions

Total mentions: 2

Testing Pleiotropy <i>vs.</i> Separate QTL in Multiparental Populations
Last synced: 4 months ago
qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations
Last synced: 4 months ago

GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 635
  • Total Committers: 3
  • Avg Commits per committer: 211.667
  • Development Distribution Score (DDS): 0.013
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Frederick Boehm f****m@g****m 627
Karl Broman k****n@g****m 7
Kyle Niemeyer k****r@g****m 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 43
  • Total pull requests: 3
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 26 minutes
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 1.28
  • Average comments per pull request: 1.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • fboehm (39)
  • HongHe0123 (4)
Pull Request Authors
  • kbroman (2)
  • kyleniemeyer (1)
Top Labels
Issue Labels
enhancement (10) bug (5) good first issue (4)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 244 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: qtl2pleio

Testing Pleiotropy in Multiparental Populations

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 244 Last month
Rankings
Forks count: 21.9%
Stargazers count: 24.2%
Dependent packages count: 29.8%
Average: 34.2%
Dependent repos count: 35.5%
Downloads: 59.7%
Maintainers (1)
frederick.boehm@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2 depends
  • MASS * imports
  • Rcpp * imports
  • dplyr * imports
  • gemma2 * imports
  • ggplot2 * imports
  • magrittr * imports
  • parallel * imports
  • rlang * imports
  • tibble * imports
  • broman * suggests
  • covr * suggests
  • devtools * suggests
  • knitr * suggests
  • mvtnorm * suggests
  • parallelly * suggests
  • qtl2 * suggests
  • rmarkdown * suggests
  • testthat * suggests