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d3b-center / annoFuse

Filter and prioritize fusion calls
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reciprocal and Domain retention #70

Closed kgaonkar6 closed 4 years ago

kgaonkar6 commented 4 years ago

checkReciprocal creates column reciprocal_exists in annotate_fusion_calls()

checkDomainStatus creates columns "DomainRetainedInGene1A" ,"DomainRetainedInGene1B" here the domainsToCheck will be given a character list of pfamIDs in fusion_driver() since it seems to be more of a project specific criteria, does that sound ok?

kinaseid<-unique(bioMartDataPfam$pfam_id[grep("kinase",bioMartDataPfam$NAME)] )

the code will check status of the domain in either Gene1A and Gene1B

kgaonkar6 commented 4 years ago

the checkDomainStatus adds columns "DomainRetainedInGene1A" ,"DomainRetainedInGene1B" by checking for overlap with domainsToCheck ( we are using kinase pfamIDS). If we set it by default = TRUE do we always check for kinase domain by default as well? I wasn't sure if we want to always check for kinase domians so made it FALSE by deafult

kgaonkar6 commented 4 years ago

Also adding the inst/extdata and demo file #66 and updating Putative driver filtering vignette