[BioC] Package SomaticCancerAlterations, import own .maf file?

Shila Ghazanfar [guest] guest at bioconductor.org
Fri Dec 13 09:37:25 CET 2013


My name is Shila Ghazanfar and I am a PhD candidate at the University of Sydney. I came across the BioC package SomaticCancerAlterations and have found it a quite useful and elegant way of handling the TCGA somatic mutation data available within the R environment.

I would like to ask if there is a capability within the package to import your own downloaded .maf file and subsequently use all the functions within the package? Reading through the package vignette as well as the User manual, this doesn't seem to be available, but I would like to know if indeed there is a way to do this?

Kind regards,

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SomaticCancerAlterations_0.99.20

loaded via a namespace (and not attached):
 [1] BiocGenerics_0.8.0   Biostrings_2.30.1    bitops_1.0-6         exomeCopy_1.8.0     
 [5] GenomicRanges_1.14.4 IRanges_1.20.6       parallel_3.0.2       Rsamtools_1.14.2    
 [9] stats4_3.0.2         stringr_0.6.2        tools_3.0.2          XVector_0.2.0       
[13] zlibbioc_1.8.0      

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