Repository hotspots
Name: hotspots
Owner: nanettec
Synopsis: Identify eQTL hotspots using permutation threshold and chi-squared test
### This is the sixth tool in the eQTL backend pipeline: 
lookup, classification, frequency, sliding window frequency, hotspots, GO enrichment

Link to the workflow (for import into Galaxy): http://chewbacca.bi.up.ac.za:8080/u/nanette/w/back-end-workflow-2

Identify the max number of eQTL expected by chance per cM using a permutation approach.

Eliminate differential gene density as an explanatory factor for eQTL hotspots, by performing a chi-squared test per bin.

* Calculate the proportion of genes to eQTLs, use this as the population estimates and test the null hypothesis that the number of genes and eQTLs in each interval is consistent.
* Mark bins where the expected number (genes + eQTLs) of every interval is not 5 or more (assumption for chi-squared test). For these bins the chi-squared test cannot be performed.

Extract lists of eQTLs linked to each unbiased eQTL hotspot.

Genome wide eQTL freqeuncy plots.
Type: unrestricted
Revision: 1:ee4662eeb8c8
This revision can be installed: True
Times cloned / installed: 269
Dependencies of this repository

Name Version Type
R_SCRIPT_PATH set_environment

Contents of this repository

Name Description Version Minimum Galaxy Version
using permutation threshold and chi-squared test 5.0.0 any

Categories
Genome-Wide Association Study - Utilities to support Genome-wide association studies