ComBat_seq cannot be found

[Zepeng-Mu]

Hi, I installed the package from GitHub repo sva-devel. I can see the document page of ComBat_seq but when I try to run the function, I got "could not find function "ComBat_seq".

[mestato]

Did you load the library? After installing the devel version, make sure you load/attach it:

library("sva")

[Zepeng-Mu]

I think I actually did. I could use the old version of ComBat for instance. Now I just clone the GitHub repo and use source to load ComBat_seq and it works.

[madhulika-EBI]

Hi, I am also not able to find ComBat_seq upon package installation. can you please make it available through Bioconductor SVA version also. Thanks

[PrincescaDorsaint]

Hi, I also cannot find the ComBat_seq function via "sva" package. Is this function no longer available?

[zhangyuqing]

@Zepeng-Mu @madhulika-EBI @PrincescaDorsaint ComBat-Seq is already available in the development version of Bioconductor, which I believe requires R > 4.0. https://www.bioconductor.org/packages/devel/bioc/html/sva.html

If you do not want to update your R version to use devel Bioconductor, you can 1) wait until the next Bioconductor release, 2) clone the GitHub repo and use source to load ComBat_seq, as @Zepeng-Mu suggests, or 3) use the sva package on my github devtools::install_github("zhangyuqing/sva-devel").

With 3), make sure to remove the previous sva installed on your laptop: remove.packages("sva") before installing. After installation, check packageVersion("sva") to make sure it is version 3.35.2. This works on my laptop, and I'm able to find ComBat_seq function. If you still can't find it, there are suggested steps you can try to fix the issue: https://stackoverflow.com/questions/7027288/error-could-not-find-function-in-r

[Bithorax]

None of the options suggested works for me. Am I the only one having this issue?

[Zepeng-Mu]

I installed sva 3.38.0 from bioconductor and it has the ComBat_seq function, but you need R 4.0.0 to successfully install the package.

[Bithorax]

Apparently, I had an issue with the installation. Now working! Thanks!

[daixiaozhuan]

I think I actually did. I could use the old version of ComBat for instance. Now I just clone the GitHub repo and use source to load ComBat_seq and it works.

How to use source to load it

[ShwetaCh]

@zhangyuqing
Apologies to bother you on this, but I tried option3 to sva-devel since I didn't want to upgrade my R completely, it does not work for me. Is it broken at the source by any chance or do I need to do anything more at my end?

> devtools::install_github("zhangyuqing/sva-devel")
Downloading GitHub repo zhangyuqing/sva-devel@HEAD
sh: 1: /bin/gtar: not found
sh: 1: /bin/gtar: not found
Error: Failed to install 'sva' from GitHub:
  error in running command
In addition: Warning messages:
1: In system(cmd) : error in running command
2: In utils::untar(tarfile, ...) :
  ‘/bin/gtar -xf '/tmp/Rtmp7pld2E/file4a0e386a4721.tar.gz' -C '/tmp/Rtmp7pld2E/remotes4a0e2f329d74'’ returned error code 127

Update: I did it the source way

[ShwetaCh]

How to use source to load it

@daixiaozhuan You can do it as below:
git clone https://github.com/zhangyuqing/ComBat-seq.git <-- on command prompt
source("/home/user/testing/ComBat-seq/ComBat_seq.R") <-- inside your R script