genewiseMAFC.py¶
-
genewiseMAFC.
enrichASE
(args)[source]¶ identify genes with differential expression between two alleles
requires: annotated SNP data (*.merged.csv) output from bedtools intersect
- How it works:
- group SNPs together by gene
- For each SNP in that gene, calculate the absolute(log2(fold change))
- take the average of absolute(log2(fold change)) values across all SNPS for that gene
- filter on:
- average read depth at variable positions for the gene
- number of SNPs in the gene
- average(absolute(log2(fold change))) for the gene
- Two optional args with no defaults change the program behaviour:
- –output <file> sends the results to file rather than stdout
- –gene <gene> yields data for every SNP in a specific gene. Without this arg, the program produces instead a summary table of all significant genes in order of priority (sorted by: average(absolute(log2(fold change))))