error with sciClone

Question

[cristinam09]

I am a very beginner with R, I have been trying to teach myself because I want to use sciClone to visualize tumor heterogeneity from NGS data. I installed the packages, downloaded the demo dataset from github, imported them into R but when I run the function

sc = sciClone(data1=v1,
+          copyNumberCalls=cn1,
+          sampleNames=names[1],
+          regionexclude=reg1)

I have this message

Error: could not find function "sciClone"

however from the function installed.packages() I see sciClone in the list.

Can somebody please help me? sorry if this is a very beginner question but I don't know what else to do, nice package I really want to use. Thank you so much!!

[ivivek_ngs]

@cristinam09 can you tell me how did you download the sciClone from the github, which are the necessary packages that are needed to download from github , am unable to understand how to download sciclone from github and use it in R in my mac locally, it is not in CRAN or Bioconductors so I have to download the package locally and then import it in the R . However my R version is 2.15. Is that compatible for SciClone?

[Devon Ryan]

Installation instructions are the first thing listed in the README file:

#install devtools if you don't have it already
install.packages("devtools")
library(devtools)
install_github("genome/bmm")
install_github("genome/sciClone")

[ivivek_ngs]

When am installing devtools it is throwing an error stating it is not built for 2.15 , do I have to upgrade to R 3.0 to use devtools and sciClone?

[ivivek_ngs]

Yes I have downloaded a new version of R and then installed sciClone, thanks a lot

Answer 1

[Devon Ryan]

Try library(sciClone). Just because you have something installed doesn't mean you have it currently loaded.

[cristinam09]

Thank you so much, it works!!

Now I have another problem to sort out :), looks like my files are not named properly, but I think I can fix this.