R: Function to read in a GATKReport

gsa.read.gatkreport {gsalib} | R Documentation

## 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 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

http://www.broadinstitute.org/gatk/guide/article?id=1244

### Examples

    test_file = system.file("inst", "extdata", "test_gatkreport.table", package = "gsalib");
    report = gsa.read.gatkreport(test_file);

[Package gsalib version 2.1 Index]