Package gsalib. R topics documented: February 20, Type Package. Title Utility Functions For GATK. Version 2.1.
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1 Package gsalib February 20, 2015 Type Package Title Utility Functions For GATK Version 2.1 Date Author Maintainer Geraldine Van der Auwera This package contains utility functions used by the Genome Analysis Toolkit (GATK) to load tables and plot data. The GATK is a toolkit for variant discovery in high-throughput sequencing data. License MIT + file LICENSE LazyLoad yes NeedsCompilation no Repository CRAN Date/Publication :09:01 R topics documented: gsalib-package gatkreport_test_v1.table gsa.read.gatkreport gsa.read.gatkreportv gsa.read.gatkreportv Index 7 1
2 2 gsalib-package gsalib-package Utility functions for GATK Details Utility functions for analysis of genome sequence data with the GATK
3 gatkreport_test_v1.table 3 Package: gsalib Type: Package Version: 2.1 Date: License: MIT LazyLoad: yes This package is primarily meant to be used programmatically by GATK tools. However the gsa.read.gatkreport() function can be used to easily read in data from a GATKReport. A GATKReport is a multi-table document generated by GATK tools. Maintainer: Geraldine Van der Auwera <vdauwera@broadinstitute.org> Examples test_file = system.file("inst", "extdata", "test_gatkreport.table", package = "gsalib"); report = gsa.read.gatkreport(test_file); gatkreport_test_v1.table Test table for version 1.x GATKReport This is a new-style GATKReport. gatkreport_test_v1.table Format Text document containing multiple tables Source GSA test data, Broad Institute
4 4 gsa.read.gatkreport gsa.read.gatkreport Function to read in a GATKReport This function reads in data from a GATKReport. A GATKReport is a document containing multiple tables produced by the GATK. Each table is loaded as a separate data.frame object in a list. gsa.read.gatkreport(filename) Arguments filename The path to the GATKReport file. Details The GATKReport format replaces the multi-file output format used by many GATK tools and provides a single, consolidated file format. This format accommodates multiple tables and is still R-loadable through this function. Value Returns a LIST object, where each key is the TableName and the value is the data.frame object with the contents of the table. If multiple tables with the same name exist, each one after the first will be given names of TableName.v1, TableName.v2,..., TableName.vN. Note This function accepts different versions of the GATKReport format by making internal calls to gsa.read.gatkreportv0() or gsa.read.gatkreportv1() as appropriate. Examples test_file = system.file("inst", "extdata", "test_gatkreport.table", package = "gsalib"); report = gsa.read.gatkreport(test_file);
5 gsa.read.gatkreportv0 5 gsa.read.gatkreportv0 Function to read in an old-style GATKReport This function reads in data from a version 0.x GATKReport. It should not be called directly; instead, use gsa.read.gatkreport() gsa.read.gatkreportv0(lines) Arguments lines The lines read in from the input file. Value Returns a LIST object, where each key is the TableName and the value is the data.frame object with the contents of the table. If multiple tables with the same name exist, each one after the first will be given names of TableName.v1, TableName.v2,..., TableName.vN. gsa.read.gatkreportv1 Function to read in a new-style GATKReport This function reads in data from a version 1.x GATKReport. It should not be called directly; instead, use gsa.read.gatkreport() gsa.read.gatkreportv1(lines) Arguments lines The lines read in from the input file.
6 6 gsa.read.gatkreportv1 Value Returns a LIST object, where each key is the TableName and the value is the data.frame object with the contents of the table. If multiple tables with the same name exist, each one after the first will be given names of TableName.v1, TableName.v2,..., TableName.vN.
7 Index Topic manip gsa.read.gatkreport, 4 gsa.read.gatkreportv0, 5 gsa.read.gatkreportv1, 5 Topic package gsalib-package, 2 gatkreport_test_v1.table, 3 gsa.read.gatkreport, 4 gsa.read.gatkreportv0, 5 gsa.read.gatkreportv1, 5 gsalib (gsalib-package), 2 gsalib-package, 2 7
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