Question: Package SomaticCancerAlterations, import own .maf file?
5.5 years ago by
Guest User • 12k
Guest User • 12k 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:  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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