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!!
•
written
by
cristinam09 •
Try library(sciClone). Just because you have something installed doesn't mean you have it currently loaded.
•
written
by
Devon Ryan
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.
•
written
by
cristinam09 •
Log in to answer this question.
@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?
Installation instructions are the first thing listed in the README file:
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?
Yes I have downloaded a new version of R and then installed sciClone, thanks a lot