h5vc-package: Managing alignment tallies using a hdf5 backend

In h5vc: 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 [e-mail]

h5vc documentation built on Nov. 8, 2020, 4:56 p.m.