Entering edit mode
Fong Chun Chan
▴
320
@fong-chun-chan-5706
Last seen 10.5 years ago
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
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