Include latex package option before documentclass in RMarkdown beamer presentation - latex

Question

I am trying to compile the following beamer presentation in rmarkdown. But when it tries to render rmarkdown document an error occurs
! LaTeX Error: Option clash for package xcolor.
I searched Internet and found out that I need to include \PassOptionsToPackage{table}{xcolor} before the line \documentclass. Applying options to already loaded package and also see here
How do I do it in RMarkdown?
---
title: "My report"
output:
beamer_presentation:
keep_tex: true
header-includes:
- \usepackage{booktabs}
- \usepackage{tabu}
- \usepackage{threeparttable}
- \usepackage{threeparttablex}
- \usepackage[normalem]{ulem}
- \usepackage[table]{xcolor}
---
```{r setup, include=FALSE}
library(knitr)
library(kableExtra)
knitr::opts_chunk$set(echo = FALSE)
```
```{r positioned_table}
dt <- mtcars[1:5, 1:6]
kable(dt) %>%
kable_styling("striped", full_width = F) %>%
column_spec(5:7, bold = T) %>%
row_spec(3:5, bold = T, color = "white", background = "#D7261E")
```
The resulting .tex file is
\PassOptionsToPackage{unicode=true}{hyperref} % options for packages loaded elsewhere
\PassOptionsToPackage{hyphens}{url}
%
\documentclass[ignorenonframetext,]{beamer}
\usepackage{pgfpages}
\setbeamertemplate{caption}[numbered]
\setbeamertemplate{caption label separator}{: }
\setbeamercolor{caption name}{fg=normal text.fg}
\beamertemplatenavigationsymbolsempty
% Prevent slide breaks in the middle of a paragraph:
\widowpenalties 1 10000
\raggedbottom
\setbeamertemplate{part page}{
\centering
\begin{beamercolorbox}[sep=16pt,center]{part title}
\usebeamerfont{part title}\insertpart\par
\end{beamercolorbox}
}
\setbeamertemplate{section page}{
\centering
\begin{beamercolorbox}[sep=12pt,center]{part title}
\usebeamerfont{section title}\insertsection\par
\end{beamercolorbox}
}
\setbeamertemplate{subsection page}{
\centering
\begin{beamercolorbox}[sep=8pt,center]{part title}
\usebeamerfont{subsection title}\insertsubsection\par
\end{beamercolorbox}
}
\AtBeginPart{
\frame{\partpage}
}
\AtBeginSection{
\ifbibliography
\else
\frame{\sectionpage}
\fi
}
\AtBeginSubsection{
\frame{\subsectionpage}
}
\usepackage{lmodern}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{textcomp} % provides euro and other symbols
\else % if luatex or xelatex
\usepackage{unicode-math}
\defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage[]{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
\usepackage{hyperref}
\hypersetup{
pdftitle={My report},
pdfborder={0 0 0},
breaklinks=true}
\urlstyle{same} % don't use monospace font for urls
\newif\ifbibliography
\setlength{\emergencystretch}{3em} % prevent overfull lines
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\setcounter{secnumdepth}{0}
% set default figure placement to htbp
\makeatletter
\def\fps#figure{htbp}
\makeatother
\usepackage{booktabs}
\usepackage{tabu}
\usepackage{threeparttable}
\usepackage{threeparttablex}
\usepackage[normalem]{ulem}
\usepackage[table]{xcolor}
\title{My report}
\date{}
\begin{document}
\frame{\titlepage}
\begin{frame}
\begin{table}[H]
\centering
\begin{tabular}{l|r|r|r|>{\bfseries}r|>{\bfseries}r|>{\bfseries}r}
\hline
& mpg & cyl & disp & hp & drat & wt\\
\hline
Mazda RX4 & 21.0 & 6 & 160 & 110 & 3.90 & 2.620\\
\hline
Mazda RX4 Wag & 21.0 & 6 & 160 & 110 & 3.90 & 2.875\\
\hline
\rowcolor[HTML]{D7261E} \textcolor{white}{\textbf{Datsun 710}} & \textcolor{white}{\textbf{22.8}} & \textcolor{white}{\textbf{4}} & \textcolor{white}{\textbf{108}} & \textcolor{white}{\textbf{93}} & \textcolor{white}{\textbf{3.85}} & \textcolor{white}{\textbf{2.320}}\\
\hline
\rowcolor[HTML]{D7261E} \textcolor{white}{\textbf{Hornet 4 Drive}} & \textcolor{white}{\textbf{21.4}} & \textcolor{white}{\textbf{6}} & \textcolor{white}{\textbf{258}} & \textcolor{white}{\textbf{110}} & \textcolor{white}{\textbf{3.08}} & \textcolor{white}{\textbf{3.215}}\\
\hline
\rowcolor[HTML]{D7261E} \textcolor{white}{\textbf{Hornet Sportabout}} & \textcolor{white}{\textbf{18.7}} & \textcolor{white}{\textbf{8}} & \textcolor{white}{\textbf{360}} & \textcolor{white}{\textbf{175}} & \textcolor{white}{\textbf{3.15}} & \textcolor{white}{\textbf{3.440}}\\
\hline
\end{tabular}
\end{table}
\end{frame}
\end{document}

Answer 1

Using very usefull comment from #samcarter, I found the exact answer. All I need is the following yaml header in my rmarkdown document:
---
title: "My report"
output:
beamer_presentation:
keep_tex: true
classoption: xcolor=table
header-includes:
- \usepackage{booktabs}
- \usepackage{tabu}
- \usepackage{threeparttable}
- \usepackage{threeparttablex}
- \usepackage[normalem]{ulem}
---

Answer 2

To use the table xcolor option with beamer on can pass this to the documentclass. In traditional latex
\documentclass[xcolor={table}]{beamer}
For markdown https://bookdown.org/yihui/rmarkdown/pdf-document.html#latex-options suggests that on can use
classoption: xcolor={table}