SomaticSignatures
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Huma Asif ▴ 90
@huma-asif-6466
Last seen 6.6 years ago
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 > > > [[alternative HTML version deleted]]
Annotation Cancer convert Annotation Cancer convert • 1.2k views
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Julian Gehring ★ 1.3k
@julian-gehring-5818
Last seen 23 months ago
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/SomaticSignature s/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 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
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