Reading an R file from GitHub

Lets say that I want to read in this R file from GitHub into R.

The first thing you have to do is locate the raw file. You can do so by clicking on the Raw button in GitHub. In this case it’s https://raw.github.com/lcolladotor/ballgownR-devel/master/ballgownR/R/infoGene.R

One would think that using source() would work, but it doesn’t as shown below:

source("https://raw.github.com/lcolladotor/ballgownR-devel/master/ballgownR/R/infoGene.R")
## Warning: unsupported URL scheme
## Error: cannot open the connection

However, thanks again to Hadley Wickham you can do so by using the devtools (Wickham & Chang, 2013 ) package.

Here is how it works:

library(devtools)
library(roxygen2)
## Needed because this file has roxygen2 comments. Otherwise you get a
## 'could not find function 'digest'' error
source_url("https://raw.github.com/lcolladotor/ballgownR-devel/master/ballgownR/R/infoGene.R")
## SHA-1 hash of file is 6c32a620799eded5d6ff0997a184843d7964724a
## Note that you can specify the SHA-1 hash to be very specific about
## which version of the file you want to read in.

We can then check that infoGene has actually been sourced:

"infoGene" %in% ls()
## [1] TRUE

That’s it! Enjoy!

Citations made with knitcitations (Boettiger, 2013 ).

Reproducibility

sessionInfo()
## R version 3.0.0 (2013-04-03)
## Platform: x86_64-apple-darwin10.8.0 (64-bit)
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] roxygen2_2.2.2      digest_0.6.3        devtools_1.2       
## [4] knitcitations_0.4-6 bibtex_0.3-5        knitr_1.2          
## 
## loaded via a namespace (and not attached):
##  [1] brew_1.0-6     evaluate_0.4.3 formatR_0.7    httr_0.2      
##  [5] memoise_0.1    parallel_3.0.0 RCurl_1.95-4.1 stringr_0.6.2 
##  [9] tools_3.0.0    whisker_0.3-2  XML_3.95-0.2   xtable_1.7-1
Avatar
Leonardo Collado-Torres
Staff Scientist II

Brain genomics #rstats coder working w/ @andrewejaffe @LieberInstitute. @lcgunam @jhubiostat @jtleek alumni. @LIBDrstats @CDSBMexico co-founder.

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