Installing crlmmCompendium package in to R, Ubuntu

Question

[hasani.iut6]

Hi,

I want to analysis genotype array of Affymetrix. I use crlmm package for doing that. In the manual paper of this package there is another package names as crlmmCompendium that should be installed. I searched a lot to installing that to R in Ubuntu but I have not succeeded yet. Is there anyone that can help me?

Manual paper:

Using the R Package crlmm for Genotyping and Copy Number Estimation

Answer 1

[Kevin Blighe]

The package was moved to GitHub: https://github.com/rscharpf/crlmmCompendium

The authors have not updated the reference to it in their published work, and neither appear to have updated their associate R packages for some time. I just tried to install but my R version is too advanced.

You can install by trying the following:

Outside R - download raw files

git clone https://github.com/rscharpf/crlmmCompendium

In R:

install.packages("./crlmmCompendium/", repos=NULL, type="source", dependencies=c("crlmm", "SNPchip", "VanillaICE"))

...or install the dependencies separately , i.e., crlmm SNPchip VanillaICE, and then run:

install.packages("./crlmmCompendium/", repos=NULL, type="source")

If you cannot get it working after that, then you may consider trying Aroma Affymetrix for the purposes of deriving copy number.

[hasani.iut6]

That's work. Thank you a lot.

[Kevin Blighe]

Amazing - good luck with the analysis.

[hasani.iut6]

Do you know how can I access to the data of the paper? because data cannot be accessed from the ncbi

[Kevin Blighe]

Did you follow this tutorial: https://biostats.bepress.com/cgi/viewcontent.cgi?article=1218&context=jhubiostat ?