An example Knitr/R Markdown document

In trena: Fit transcriptional regulatory networks using gene expression, priors, machine learning

A minimal R Markdown example

A quote:

Markdown is not LaTeX.

To compile me, run this in R:

library(knitr)
knit('001-minimal.Rmd')

See output here.

code chunks

A paragraph here. A code chunk below (remember the three backticks):

1+1
.4-.7+.3 # what? it is not zero!

graphics

It is easy.

plot(1:10)
hist(rnorm(1000))

inline code

Yes I know the value of pi is r pi, and 2 times pi is r 2*pi.

math

Sigh. You cannot live without math equations. OK, here we go: $\alpha+\beta=\gamma$. Note this is not supported by native markdown. You probably want to try RStudio, or at least the R package markdown, or the function knitr::knit2html().

nested code chunks

You can write code within other elements, e.g. a list

1. foo is good r strsplit('hello indented world', ' ')[[1]]
2. bar is better

Or inside blockquotes:

Here is a quote, followed by a code chunk:

r x = 1:10 rev(x^2)

conclusion

Nothing fancy. You are ready to go. When you become picky, go to the knitr website.

trena documentation built on Nov. 15, 2020, 2:07 a.m.