69 lines
1.9 KiB
R
69 lines
1.9 KiB
R
\name{gsalib-package}
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\alias{gsalib-package}
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\alias{gsalib}
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\docType{package}
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\title{
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GATK utility analysis functions
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}
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\description{
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Utility functions for analyzing GATK-processed NGS data
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}
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\details{
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This package contains functions for working with GATK-processed NGS data. These functions include a command-line parser that also allows a script to be used in interactive mode (good for developing scripts that will eventually be automated), a proportional Venn diagram generator, convenience methods for parsing VariantEval output, and more.
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}
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\author{
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Genome Sequencing and Analysis Group
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Medical and Population Genetics Program
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Maintainer: Kiran Garimella
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}
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\references{
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GSA wiki page: http://www.broadinstitute.org/gsa/wiki
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GATK help forum: http://www.getsatisfaction.com/gsa
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}
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\examples{
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## get script arguments in interactive and non-interactive mode
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cmdargs = gsa.getargs( list(
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requiredArg1 = list(
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value = NA,
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doc = "Documentation for requiredArg1"
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),
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optionalArg1 = list(
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value = 3e9,
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doc = "Documentation for optionalArg1"
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)
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) );
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## plot a proportional Venn diagram
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gsa.plot.venn(500, 250, 0, 100);
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## read a GATKReport file
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report = gsa.gatk.report("/path/to/my/output.gatkreport");
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## emit a message
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gsa.message("This is a message");
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## emit a warning message
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gsa.message("This is a warning message");
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## emit an error message
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gsa.message("This is an error message");
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## read the SQUID metrics for a given sequencing project (internal to the Broad only)
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s = gsa.read.squidmetrics("C427");
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## read command-line arguments
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cmdargs = gsa.getargs(
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list(
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file = list(value="/my/test.vcf", doc="VCF file"),
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verbose = list(value=0, doc="If 1, set verbose mode"),
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test2 = list(value=2.3e9, doc="Another argument that does stuff")
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),
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doc="My test program"
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);
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}
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\keyword{ package }
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