[BioC] SomaticSignatures

[Julian Gehring]

Hi Huma,

As it is stated in the vignette:

"The starting point of the analysis is a VRanges object which describes 
the somatic variants in terms of their genomic locations as well as 
reference and alternative alleles. For more details about this class and 
how to construct it, please see the documentation of the 
VariantAnnotation package."

It is up to you how you import your variant calls and create the VRanges 
object.  If you have a VCF file, the easiest way would be the 
'readVcfAsVRanges' method in the 'VariantAnnotation' package, which is 
closely related to the 'readVcf' function that you have been using 
before.  You can find an example in the vignette of the current 
developer version, 
http://bioconductor.org/packages/devel/bioc/vignettes/SomaticSignatures/inst/doc/SomaticSignatures-vignette.html#sec-5: 
'Use case: Analyzing Own Mutation Calls'.

Best wishes
Julian


On 04.07.2014 05:25, Huma Asif wrote:
> 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 toÂ
> 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 followÂ
>> 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 followÂ
> 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