Repository frequency_sliding
Owner: nanettec
Synopsis: Sliding Window frequency of eQTLs and genes
### This is the fourth 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

Combine x cM intervals (size of lookup bins; for example 2 cM), to be used in a sliding window approach.

For 2 cM lookup bins:

* For two intervals per sliding window, intervals smaller than 2 cM are combined with its two flanking 2 cM intervals.
Calculate the number of eQTLs per sliding window (4 - 5.9 cM intervals).
Calculate the number of genes per sliding window (4 - 5.9 cM intervals).

* For three intervals per sliding window, intervals smaller than 2 cM are combined with 3 flanking 2 cM intervals.
Calculate the number of eQTLs per sliding window (6 - 7.9 cM intervals).
Calculate the number of genes per sliding window (6 - 7.9 cM intervals).
Type: unrestricted
Revision: 1:18e59d049951
This revision can be installed: True
Times cloned / installed: 203
Dependencies of this repository

Name Version Type
R_SCRIPT_PATH set_environment

Contents of this repository

Name Description Version Minimum Galaxy Version
of eQTLs and genes 5.0.0 any

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