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<h1 class="title toc-ignore">Prj01_RL_pheno_qtl2_DO_11092020_69k</h1>
<h4 class="author">Hao He</h4>
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<strong>Last updated:</strong> 2022-09-07
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<p>
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 6 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 1
</p>
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<strong>Knit directory:</strong> <code>csna_workflow/</code> <span class="glyphicon glyphicon-question-sign" aria-hidden="true" title="This is the local directory in which the code in this file was executed."> </span>
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This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis was created with <a
href="https://github.com/jdblischak/workflowr">workflowr</a> (version 1.6.2). The <em>Checks</em> tab describes the reproducibility checks that were applied when the results were created. The <em>Past versions</em> tab lists the development history.
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRMarkdownfilestronguptodate"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>R Markdown file:</strong> up-to-date </a>
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<p>Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.</p>
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<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongSeedstrongcodesetseed20190922code"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Seed:</strong> <code>set.seed(20190922)</code> </a>
</p>
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<div class="panel-body">
<p>The command <code>set.seed(20190922)</code> was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.</p>
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<p>Great job! Recording the operating system, R version, and package versions is critical for reproducibility.</p>
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</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
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These are the previous versions of the repository in which changes were made to the R Markdown (<code>analysis/Prj01_RL_pheno_qtl2_DO_11092020_69k.Rmd</code>) and HTML (<code>docs/Prj01_RL_pheno_qtl2_DO_11092020_69k.html</code>) files. If you’ve configured a remote Git repository (see <code>?wflow_git_remote</code>), click on the hyperlinks in the table below to view the files as they were in that past version.
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html
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Prj01_RL_pheno_qtl2_DO_11092020_69k
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<p><strong>Last update:</strong> 2022-09-07</p>
<div id="loading-libraries" class="section level3">
<h3>loading libraries</h3>
<pre class="r"><code>library(ggplot2)
library(gridExtra)
library(GGally)
library(parallel)
library(qtl2)
library(parallel)
library(survival)
library(regress)
library(abind)
library(openxlsx)
library(tidyverse)
rz.transform <- function(y) {
rankY=rank(y, ties.method="average", na.last="keep")
rzT=qnorm(rankY/(length(na.exclude(rankY))+1))
return(rzT)
}
setwd("/projects/csna/csna_workflow/")</code></pre>
</div>
<div id="read-phenotype-data" class="section level3">
<h3>Read phenotype data</h3>
<pre class="r"><code>#Prj01_RL_pheno_qttl2_DO_11092020
pheno <- readr::read_csv("data/pheno/Prj01_RL_pheno_qttl2_DO_11092020.csv", na = c("N/A", "NA"))
pheno <- pheno %>%