Dear All,
i have tried all steps in somatic signature vignette and it run successfully and i am understanding also because may be i have started learning R language. it is using data from somatic cancer alteration package. some questions: if i want to follow this guide i think i need to 
first convert data into rda extension ( as i have output in vcf file)
second question about accessing data:
how can i import my data into data or metadata package

when i put vcf file in variant annotation extdata folder and follow 
> library(VariantAnnotation)
> fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
> vcf <- readVcf(fl, "hg19")
> vcf
i can get all results as in tutorial, so can if i put my fileswith rds extension and follow 
sca_metadata = scaMetadata()
print(sca_metadata)
can i get the desired output

still confused about data and Metadata package is it necessary to convert vcf into rds and rda to access somatic signature



Huma


>________________________________
> From: Martin Morgan <mtmorgan@fhcrc.org>
>To: Huma Asif <humaasif79@yahoo.com>; Dan Tenenbaum <dtenenba@fhcrc.org> 
>Cc: "bioconductor@r-project.org list" <bioconductor@r-project.org>; Steve Lianoglou <lianoglou.steve@gene.com> 
>Sent: Tuesday, April 1, 2014 7:11 PM
>Subject: Re: [BioC] SomaticSignatures
> 
>
>I think the errors related to Biostrings
>
>On 04/01/2014 01:13 PM, Huma Asif wrote:
>
>> * installing *source* package ‘BiocParallel’ ...
>> ** R
>> ** inst
>> ** preparing package for lazy loading
>> Error in readRDS(nsInfoFilePath) : error reading from connection
>> ERROR: lazy loading failed for package ‘BiocParallel’
>
>I really don't know what is causing this, but can only guess that it is a 
>corrupt file from a previous installation attempt. You might try
>
>   rm -rf /home/asif/R/i686-pc-linux-gnu-library/3.1/BiocParallel
>
>> * installing *source* package ‘Biostrings’ ...
>> ** libs
>...
>> -pc-linux-gnu-library/3.1/XVector/include"   -fpic  -g -O2  -c io_utils.c -o
>> io_utils.o
>> io_utils.c:18:19: fatal error: bzlib.h: No such file or directory
>> compilation terminated.
>> gmake: *** [io_utils.o] Error 1
>
>Address this (and perhaps subsequent errors relating to unavailability of 
>Biostrings) by installing the system dependency
>
>   sudo apt-get install libbz2-dev
>
>(my understanding is that a revision to the devel version of Biostrings will not 
>require this dependency).
>
>Martin
>-- 
>Computational Biology / Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N.
>PO Box 19024 Seattle, WA 98109
>
>Location: Arnold Building M1 B861
>Phone: (206) 667-2793
>
>
>
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