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

Julian Gehring julian.gehring at embl.de
Fri Dec 13 10:01:43 CET 2013

Hi Shila,

The 'SomaticCancerAlterations' package has the functions for importing 
from a MAF file and converting to a 'GRanges' object.  Since they are 
only used internally, they are not exported and thus not visible in the 
man pages.  You can find them in 'R/import-functions.R', the most 
relevant functions are '.read_maf' and '.maf2gr'.  Further, 
'.validate_maf' implements some basic checks for the consistency of the 
MAF file.  You can call these functions with e.g. 

At the moment, they are only used internally for importing the TCGA 
data.  If you (and also others) are interested, I can think about 
documenting and exporting them.  The main reason why I did not do this 
so far is mainly that there is no strict specification of MAF files. 
The TCGA provides some, but even most MAF files from the TCGA project 
itself fail their own validation scheme.  Writing a parser that can 
handle them all would take some more time.

Best wishes

On 12/13/2013 09:37 AM, Shila Ghazanfar [guest] wrote:
> Hi,
> 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,
> Shila
>   -- output of sessionInfo():
>> sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> locale:
> [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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