[BioC] Package SomaticCancerAlterations, import own .maf file?
julian.gehring at embl.de
Fri Dec 13 10:01:43 CET 2013
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.
On 12/13/2013 09:37 AM, Shila Ghazanfar [guest] wrote:
> 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():
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>  LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
>  LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
>  LC_TIME=English_Australia.1252
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  SomaticCancerAlterations_0.99.20
> loaded via a namespace (and not attached):
>  BiocGenerics_0.8.0 Biostrings_2.30.1 bitops_1.0-6 exomeCopy_1.8.0
>  GenomicRanges_1.14.4 IRanges_1.20.6 parallel_3.0.2 Rsamtools_1.14.2
>  stats4_3.0.2 stringr_0.6.2 tools_3.0.2 XVector_0.2.0
>  zlibbioc_1.8.0
> Sent via the guest posting facility at bioconductor.org.
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