| Type: | Package |
| Title: | Utility Functions for 'GATK' |
| Version: | 2.2.1 |
| Date: | 2022-10-07 |
| Author: | Kiran Garimella |
| Maintainer: | Louis Bergelson <louisb@broadinstitute.org> |
| Description: | Provides 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. |
| URL: | https://gatk.broadinstitute.org/hc/en-us, https://github.com/broadinstitute/gatk, https://github.com/broadinstitute/gsalib/ |
| BugReports: | https://github.com/broadinstitute/gsalib/issues |
| License: | MIT + file LICENSE |
| LazyLoad: | yes |
| NeedsCompilation: | no |
| Repository: | CRAN |
| Date/Publication: | 2022-10-07 22:50:05 UTC |
| Packaged: | 2022-10-07 18:48:27 UTC; louisb |
Utility functions for GATK
Description
Utility functions for analysis of genome sequence data with the GATK
Details
| Package: | gsalib |
| Type: | Package |
| Version: | 2.2 |
| Date: | 2015-03-17 |
| 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.
Author(s)
Kiran Garimella
Maintainer: Louis Bergelson <louisb@broadinstitute.org>
References
https://gatk.broadinstitute.org/hc/en-us/articles/360035532172-GATKReport-and-gsalib
Examples
test_file = system.file("inst", "extdata", "test_gatkreport.table", package = "gsalib");
report = gsa.read.gatkreport(test_file);
Function to read in a GATKReport
Description
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.
Usage
gsa.read.gatkreport(filename)
Arguments
filename |
The path to the GATKReport file. |
Details
The GATKReport format replaces the multi-file output format used previously 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.
Author(s)
Kiran Garimella
References
https://gatk.broadinstitute.org/hc/en-us/articles/360035532172-GATKReport-and-gsalib
Examples
test_file = system.file("extdata", "test_gatkreport.table", package = "gsalib");
report = gsa.read.gatkreport(test_file);
Function to read in an old-style GATKReport
Description
This function reads in data from a version 0.x GATKReport. It should not be called directly; instead, use gsa.read.gatkreport()
Usage
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.
Author(s)
Kiran Garimella
References
https://gatk.broadinstitute.org/hc/en-us/articles/360035532172-GATKReport-and-gsalib
Function to read in a new-style GATKReport
Description
This function reads in data from a version 1.x GATKReport. It should not be called directly; instead, use gsa.read.gatkreport()
Usage
gsa.read.gatkreportv1(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.
Author(s)
Kiran Garimella
References
https://gatk.broadinstitute.org/hc/en-us/articles/360035532172-GATKReport-and-gsalib
Reshape a Concordance Table
Description
Given a GATKReport generated by GenotypeConcordance (as output by gsa.read.gatkreport), this function reshapes the concordance for a specified sample into a matrix with the EvalGenotypes in rows and the CompGenotypes in columns (see the documentation for GenotypeConcordance for the definition of Eval and Comp)
Usage
gsa.reshape.concordance.table(
report,
table.name="GenotypeConcordance_Counts",
sample.name="ALL")
Arguments
report |
A GATKReport as output by |
table.name |
The table name in the GATKReport to reshape. Defaults to "GenotypeConcordance_Counts", but could also be one of the proportion tables ("GenotypeConcordance_EvalProportions", "GenotypeConcordance_CompProportions"). This value can also be |
sample.name |
The sample name within |
Value
Returns a two-dimensional matrix with Eval genotypes in the rows and Comp genotypes in the columns. The genotypes themselves (HOM_REF, NO_CALL, etc) are specified in the row/col names of the matrix.
Author(s)
Phillip Dexheimer
See Also
Examples
test_file = system.file("extdata", "test_genconcord.table", package = "gsalib")
report = gsa.read.gatkreport(test_file)
gsa.reshape.concordance.table(report)
## Output looks like:
## CompGenotypes
##EvalGenotypes NO_CALL HOM_REF HET HOM_VAR UNAVAILABLE MIXED
## NO_CALL 0 0 0 0 0 0
## HOM_REF 0 0 0 0 0 0
## HET 0 0 13463 90 3901 0
## HOM_VAR 0 0 2935 18144 4448 0
## UNAVAILABLE 0 0 2053693 1326112 11290 0
## MIXED 0 0 0 0 0 0
Internal gsalib objects
Description
Internal gsalib objects.
Details
These are not to be called by the user.