h5vc-package {h5vc} | R Documentation

## Managing alignment tallies using a hdf5 backend

### Description

This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files. For detail see vignettes shipped with this package.

### Details

Package: | h5vc
Type: | Package
Version: | 1.0.4
Date: | 2013-10-11
License: | GPL (>= 3)

This package is desgned to facilitate the analysis of genomics data through tallies stored in a HDF5 file. Within a HDF5 file the tally is simply a table of bases times genomic positions listing for each position the count of each base observed as a mismatch in the sample at any given position. Strand and sample are additional dimension in this array, which leads to a 4D-array called 'Counts'. The total coverage is stored in a separate array of 3 dimensions (Sample x Strand x Genomic Position) called 'Coverages', there is a 3 dimensional 'Deletions' array and a 1D-vector encoding the reference base ('Reference'). Those 4 arrays are stored as datasets within a HDF5 tally file in which the group-structure of the tally file encodes for the organisatorial levels of 'Study' and 'Chromosome'. For details on the layout of HDF5 files visit (http://www.hdfgroup.org), a short description is given in the vignettes.

Creating those HDF5 tally files can be accomplished from within R or through a Python script that will generate a tally file from a set of .bam files. The workflow is described in the vignettes `h5vc.creating.tallies` and `h5vc.creating.tallies.within.R`.

### Author(s)

Paul Pyl Maintainer: Paul Pyl pyl@embl.de

[Package h5vc version 2.28.0 Index]