| ### 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. |
hg clone https://toolshed.g2.bx.psu.edu/repos/nanettec/hotspots
| Name | Version | Type | |
|---|---|---|---|
| R_SCRIPT_PATH | set_environment | ||
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| using permutation threshold and chi-squared test | 5.0.0 | any | |