AllelicImbalance-package: A package meant to provide all basic functions for...
In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description Details Overview - standard procedure Author(s) References See Also

Package AllelicImbalance has functions for importing, filtering and plotting high-throughput data to make an allele specific expression analysis. A major aim of this package is to provide functions to collect as much information as possible from regions of choice, and to be able to explore the allelic expression of that region in detail.

Package:	AllelicImbalance
Type:	Package
Version:	1.2.0
Date:	2014-08-24
License:	GPL-3

Start out creating a GRange object defining the region of interest. This can also be done using getAreaFromGeneNames providing gene names as arguments. Then use BamImpGAList to import reads from that reagion and find potential SNPs using scanForHeterozygotes. Then retrieve the allele counts of heterozygote sites by the function getAlleleCount. With this data create an ASEset. At this point all pre-requisites for a 'basic' allele specific expression analysis is available. Two ways to go on could be to apply chisq.test or barplot on this ASEset object.

Author: Jesper Robert Gadin Author: Lasse Folkersen

Maintainer: Jesper Robert Gadin <j.r.gadin@gmail.com>

Reference to published application note (work in progress)