Perfect thanks! On Wed, Feb 5, 2014 at 2:46 PM, Michael Lawrence <lawrence.michael@gene.com>wrote: > subsetByOverlaps(vcf, myRanges) > > > > On Wed, Feb 5, 2014 at 2:22 PM, Fong Chun Chan <fongchun@alumni.ubc.ca>wrote: > >> Hi, >> >> I have question regarding accessing particular ranges of a VCF file that >> I've loaded into R. >> >> The VCF file that I've load is relatively small (~8MB). And I would like >> to >> take subsets of the vcf file that falls into a particular genomic range. >> Reading the tutorial shows that how I may use the "params" parameter in >> the >> readVcf() function for this. But this requires me to generate a tabix file >> for the vcf. I was under the impression that this is useful for big vcf >> situations. >> >> But given the fact that I've been able to load the entire VCF file into >> memory already, I don't see an easy way to just generate a subset of the >> vcf file given a set of genomic ranges. Is there no way to do this without >> having to first generate a tabix file? >> >> Thanks, >> >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 >> LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C >> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel grid stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] VariantAnnotation_1.8.10 Rsamtools_1.14.2 Biostrings_2.30.1 >> GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 >> BiocGenerics_0.8.0 reshape2_1.2.2 ggplot2_0.9.3.1 >> dplyr_0.1 mclust_4.2 stringr_0.6.2 >> plyr_1.8 xtable_1.7-1 >> [15] fields_6.9.1 maps_2.3-6 spam_0.40-0 >> knitr_1.5 argparse_0.5.3 proto_0.3-10 >> vimcom.plus_0.9-92 setwidth_1.0-3 colorout_0.9-9 >> >> loaded via a namespace (and not attached): >> [1] AnnotationDbi_1.24.0 assertthat_0.1 Biobase_2.22.0 >> biomaRt_2.18.0 bitops_1.0-6 BSgenome_1.30.0 >> colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 >> digest_0.6.4 evaluate_0.5.1 formatR_0.10 >> GenomicFeatures_1.14.2 getopt_1.20.0 gtable_0.1.2 >> [16] labeling_0.2 MASS_7.3-29 munsell_0.4.2 >> RColorBrewer_1.0-5 Rcpp_0.10.6 RCurl_1.95-4.1 >> rjson_0.2.13 RSQLite_0.11.4 rtracklayer_1.22.3 >> scales_0.2.3 stats4_3.0.2 tools_3.0.2 >> XML_3.98-1.1 zlibbioc_1.8.0 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]