In PriceLab/TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

Some introductory test

In creating a vignette, these code & output display options are useful:

1. no code display, no output
2. display code, but not output
3. display code with R prompt, but not output
4. display code and output
5. no code display, just the output
6. tasteful display of a data.frame
7. tasteful display of a data.frame, no ode
8. show a previously created image

1. execute code: no code display, no output

{r label goes here, include=FALSE}

library(trena)

2. execute code, display code, no output

library(limma)

3. show R prompt, execute code, display code, no output

library(limma)
2 + 1

5. no code display, just the output

sprintf("variant %d", 2 + 3)

6. tasteful display of a data.frame

knitr::kable(mtcars[1:5,], caption='mtcars')

7. tasteful display of a data.frame, no code, no caption

knitr::kable(mtcars[1:5,])

8. show png image file

knitr::include_graphics("igvR-nfe2-regulation.png")

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.

PriceLab/TReNA documentation built on March 21, 2023, 1:57 p.m.