getAdGenetics <- function(synId='syn10338156'){
moduleSet <- synapser::synTableQuery(paste0("SELECT DISTINCT ModuleNameFull, Module, method, brainRegion from ",synId))$asDataFrame()
#moduleSet <- moduleSet[,-c(1,2)]
colnames(moduleSet)[c(3:4)] <- c('ModuleMethod','ModuleBrainRegion')
#magma enrichments
magmaResults <- synapser::synTableQuery("SELECT * FROM syn10380432")$asDataFrame()
magmaResults <- magmaResults[,-c(1,2)]
magmaResults <- dplyr::select(magmaResults,SET,BETA,P)
colnames(magmaResults) <- c('ModuleNameFull',
'GeneSetEffect',
'GeneSetAssociationStatistic')
magmaResults$GeneSetName <- rep('MAGMA',nrow(magmaResults))
magmaResults$GeneSetCategoryName <- rep('genetics',nrow(magmaResults))
magmaResults$GeneSetADLinked <- rep(TRUE,nrow(magmaResults))
magmaResults$GeneSetBrainRegion <- rep(NA,nrow(magmaResults))
magmaResults$GeneSetDirectionAD <- rep(NA,nrow(magmaResults))
magmaResults <- dplyr::select(magmaResults,
ModuleNameFull,
GeneSetName,
GeneSetCategoryName,
GeneSetAssociationStatistic,
GeneSetEffect,
GeneSetBrainRegion,
GeneSetDirectionAD,
GeneSetADLinked)
#####merge magma results with the module set given the schema
moduleSummary <- dplyr::left_join(moduleSet,
magmaResults)
#add adjustd pvalue by brain region and gene set category
moduleSummary <- AMPAD::splitByBrainRegionAdjustPvalue(moduleSummary)
#####igap, dbgap, and genecards for ad genes enrichments
#source('enrichmentAnalysis/run_amp_ad_enrichment.R')
genesets1 <- synapser::synGet('syn5923958')
load(genesets1$path)
dbgap <- AMPAD::pullReferenceGeneSets("http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName=dbGaP")
#kegg, wikipathways, biocarta, panther, jensen_diseases, omim_disease, omim_expanded
kegg <- AMPAD::pullReferenceGeneSets("http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName=KEGG_2016")
wikipathways <- AMPAD::pullReferenceGeneSets("http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName=WikiPathways_2016")
jensen_diseases <- AMPAD::pullReferenceGeneSets("http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName=Jensen_DISEASES")
biocarta <- AMPAD::pullReferenceGeneSets("http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName=BioCarta_2016")
panther <- AMPAD::pullReferenceGeneSets("http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName=Panther_2016")
omim_disease <- AMPAD::pullReferenceGeneSets("http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName=OMIM_Disease")
omim_expanded <- AMPAD::pullReferenceGeneSets("http://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName=OMIM_Expanded")
adList <- GeneSets$Alzheimers$`AD:GeneticLoci`
adList <- c(adList,'HLA-DRB5','HLA-DRB1')
adList <- adList[-which(adList=='HLA-DRB5-DRB1')]
adList <- adList[-which(adList=='PSEN1' | adList =='PSEN2' | adList =='APP' | adList == 'P2K2B')]
adList <- list(igap = adList)
adList$dbgap <- dbgap$`Alzheimer Disease`
adList$kegg <- kegg$`Alzheimer's disease_Homo sapiens_hsa05010`
adList$wikipathwaysMouse <- wikipathways$`Alzheimers Disease_Mus musculus_WP2075`
adList$wikipathwaysHuman <- wikipathways$`Alzheimers Disease_Homo sapiens_WP2059`
adList$jensenDisease <- jensen_diseases$`Alzheimer's_disease`
adList$biocarta <- biocarta$`Deregulation of CDK5 in Alzheimers Disease_Homo sapiens_h_p35alzheimersPathway`
adList$pantherAmyloid <- panther$`Alzheimer disease-amyloid secretase pathway_Homo sapiens_P00003`
adList$pantherPresenilin <- panther$`Alzheimer disease-presenilin pathway_Homo sapiens_P00004`
adList$omim <- omim_disease$`alzheimer_disease`
adList$omimExpanded <- omim_expanded$`alzheimer_disease`
genecardsObj <- synapser::synGet('syn10507702')
genecards <- data.table::fread(genecardsObj$path,data.table=F)
adList$genecards <- genecards$`Gene Symbol`
adTest <- AMPAD::run_amp_ad_enrichment2(adList,
'genetics',
manifestId=synId)
adTest <- dplyr::select(adTest,
ModuleNameFull,
category,
geneSet,
fisherPval,
fisherOR)
colnames(adTest) <- c('ModuleNameFull',
'GeneSetName',
'GeneSetCategoryName',
'GeneSetAssociationStatistic',
'GeneSetEffect')
adTest$GeneSetADLinked <- rep(TRUE,nrow(adTest))
adTest$GeneSetBrainRegion <- rep(NA,nrow(adTest))
adTest$GeneSetDirectionAD <- rep(NA,nrow(adTest))
adTestSummary <- dplyr::left_join(moduleSet,
adTest)
adTestSummary <- AMPAD::splitByBrainRegionAdjustPvalue(adTestSummary)
#View(adTestSummary)
moduleSummary <- rbind(moduleSummary,adTestSummary)
moduleSummary$EvidenceClass <- 'genetics'
return(moduleSummary)
}
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