ANalysis of Expression VAriance
Package developed by: Pejman Mohammadi ([email protected]). See our paper for method descritions.
This Matlab package allows you to estimate the amount of genetic variation in regulation in a population (Vg) using a population AE data. Run_Example.m allows you to do a demo run of ANEVA on a set of 20 sample allelic expression data files. The package includes all inputs and output for the example data. Please feel free to reach out if you have trouble running this on your data we're always interested in calculating reference Vg for any dataset.
To run the demo you have to first decompress all data files (gunzip -r ANEVA/01_Data). Also you should include Pejtools in your Matlab path.
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If you don't know how to generate ASE data, you can start here. Note: This model assumes variant level ASE data and is not compatible with haplotypic read counts such as Phaser data.
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You can download our pre-calculated Vg estimates for available datasets at Datasets/Reference_Vg_Estimates.