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LinkageIO / Camoco

Camoco is a fully-fledged software package for building co-expression networks and analyzing the overlap interactions among genes.
MIT License
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SNP to gene mapping can sometimes mess up overlap when genes overlap. #82

Open schae234 opened 6 years ago

schae234 commented 6 years ago

By default a SNP to gene mapping of Loci to themselves (window=1 and flank=0), but when input genes have overlapping genes (on the opposite strand) a SNP to gene mapping of genes to themselves will yield additional genes.

Consider:

import camoco as co
cob = co.COB('ZmRoot')
loci = ['GRMZM2G051771', 'GRMZM5G869572', 'GRMZM2G121868', 'GRMZM2G122139', 'GRMZM2G050774', 'GRMZM2G127034', 'GRMZM2G304274', 'GRMZM2G139198', 'GRMZM2G162954', 'GRMZM2G022740']
loci = cob.refgen.from_ids(loci)
len(loci) # 10
len(cob.refgen.candidate_genes(loci,flank_limit=0)) #11