unable to install HoneyBADGER packge

[hmassalha]

Dear Jean,
I have problems to install HoneyBADGER packge. I tried using your recommended code lines:

require(devtools)
devtools::install_github('JEFworks/HoneyBADGER')

and get the following error:

> require(devtools)
Loading required package: devtools
Warning message:
package ‘devtools’ was built under R version 3.4.3 
> devtools::install_github('JEFworks/HoneyBADGER')
Downloading GitHub repo JEFworks/HoneyBADGER@master
from URL https://api.github.com/repos/JEFworks/HoneyBADGER/zipball/master
Installing HoneyBADGER
"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  "C:/Users/Hassan/AppData/Local/Temp/RtmpEl8p7L/devtools18d0487b12d8/JEFworks-HoneyBADGER-28b51c9"  \
  --library="C:/Program Files/R/R-3.4.1/library" --install-tests 

ERROR: dependencies 'GenomicRanges', 'ChIPseeker' are not available for package 'HoneyBADGER'
* removing 'C:/Program Files/R/R-3.4.1/library/HoneyBADGER'
Installation failed: Command failed (1)

Do you have any suggestion why I am getting this?

Thanks a lot, HM

[JEFworks]

Hi HM,

GenomicRanges and ChIPseeker are both available through Bioconductor and not CRAN, so you will need to install them separately first using Bioconductor:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")
biocLite("ChIPseeker")

Best,
Jean

[hmassalha]

Thanks Jean for your fast response.
I managed to install all the required packages and the HoneyBADGER. Would it be possible to provide a text file that includes a very brief explanation for the different outputs of this pipeline, especially in how to prepare the dataset to be processed with HoneyBADGER. As I am new for this type of analysis, it is difficult for me to follow the type, quality and required information for the analysis.
Thanks a lot, HM

[JEFworks]

Hi HM,

Excellent.

There is a tutorial available on how to prepare matrices of heterozygous SNP counts from bam files: http://jef.works/HoneyBADGER/Preparing_Data.html

Please see if that tutorial is sufficient and if you have additional suggestions and questions, feel free to make another issue.

Best,
Jean