AllelicImbalance-package: A package meant to provide all basic functions for high-throughput allele
specific expression analysis
Description
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.
Overview - standard procedure
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.Details
| Package: |
| AllelicImbalance |
| Type: |
| Package |
|
Version: |
| 1.2.0 |
| Date: |
| 2014-08-24 |
| License: |
| GPL-3 |
References
Reference to published application note (work in progress)