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taylor-lab / hotspots

Identifying recurrent mutations in cancer
http://www.ncbi.nlm.nih.gov/pubmed/26619011
GNU Affero General Public License v3.0
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how to get indel hotspot with this software #15

Open feihongloveworld opened 4 years ago

feihongloveworld commented 4 years ago

hi sir: there are many indel hotspot discovery in the paper of "Accelerating discovery of functional mutant alleles in cancer" as below:

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We identified 1,165 statistically significant hotspot mutations of which 80% arose in 1 in 1,000 or fewer patients. Of 55 recurrent in-frame indels, we validated that novel AKT1 duplications induced pathway hyperactivation and conferred AKT inhibitor sensitivity.

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but the hotspot soft will Discard the ins and del in soft script. how can i get indel hotpsot in mydata？ thanks

feihongloveworld commented 4 years ago

there is a code line in "funcs.R" as below:

maf=maf[ which(!maf$Variant_Type%in%c('INS','DEL')), ]