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Merge pull request #59 from ncats/patch-enrich-speed
Patch enrich speed
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| Original file line number | Diff line number | Diff line change |
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| # RaMP Reaction Queries | ||
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| #' getReactionsForAnalytes | ||
| #' | ||
| #' @param analytes list of analytes | ||
| #' @param analyteType analyte type, 'metabolites' (default), 'genes' or 'both' | ||
| #' @param namesOrIds indicates if input analyte list contains identifiers or analyte names | ||
| #' @param onlyHumanMets boolean to only return pathways containing only human metabolites (ChEBI ontology) (dev in progress) | ||
| #' @param humanProtein boolean to only control pathways catalyzed by a human proteins (having human Uniprot) (dev in progress) | ||
| #' @param includeTransportRxns if TRUE, returns metabolic and transport reactions | ||
| #' @param rxnDirs character vector of length > 1, specifying reaction directions to return c("UN", "LR", "RL", "BD", "ALL"), default = c("UN"). | ||
| #' | ||
| #' @return a list of reaction information on each input analyte, separate data.frame for metabolites, genes, and common reactions | ||
| #' @export | ||
| getReactionsForAnalytes <- function(analytes, analyteType='metabolites', namesOrIds='ids', onlyHumanMets=F, humanProtein=F, includeTransportRxns=F, rxnDirs=c("UN")) { | ||
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| genes <- data.frame() | ||
| metabolites <- data.frame() | ||
| mdf <- data.frame() | ||
| gdf <- data.frame() | ||
| if(namesOrIds == 'ids') { | ||
| analyteSourceInfo <- getRampSourceInfoFromAnalyteIDs(analytes) | ||
| resultGenes <- analyteSourceInfo[analyteSourceInfo$geneOrCompound == 'gene',] | ||
| resultMets <- analyteSourceInfo[analyteSourceInfo$geneOrCompound == 'compound',] | ||
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| if(!is.null(resultMets) && nrow(resultMets)>0) { | ||
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| print("Retrieving reactions for compounds") | ||
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| mets <- resultMets[,c('sourceId', 'rampId')] | ||
| rampIds <- unique(unlist(mets$rampId)) | ||
| mdf <- getReactionsForRaMPCompoundIds(rampCompoundIds=rampIds, onlyHumanMets=onlyHumanMets, humanProtein=humanProtein, includeTransportRxns=includeTransportRxns, rxnDirs=rxnDirs) | ||
| if(nrow(mdf) > 0) { | ||
| mdf <- merge(mets, mdf, by.x='rampId', by.y='ramp_cmpd_id') | ||
| } | ||
| } | ||
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| if(!is.null(resultGenes) && nrow(resultGenes)>0) { | ||
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| print("Retrieving reactions for genes/proteins") | ||
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| genes <- resultGenes[,c('sourceId', 'rampId')] | ||
| rampIds <- unique(unlist(genes$rampId)) | ||
| gdf <- getReactionsForRaMPGeneIds(rampGeneIds=rampIds, onlyHumanMets=onlyHumanMets, humanProtein=humanProtein, includeTransportRxns) | ||
| if(nrow(gdf) > 0) { | ||
| gdf <- merge(genes, gdf, by.x='rampId', by.y='ramp_gene_id') | ||
| } | ||
| } | ||
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| # if(!is.null(resultMets) && ncol(resultMets)>0) { | ||
| # metatabolites <- resultMets[,c('sourceId', 'rampId')] | ||
| # } | ||
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| } else { # query on names | ||
| # do we have a helper function to get ramp ids from names? | ||
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| } | ||
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| resultList <- list() | ||
| resultList[['met2rxn']] <- mdf | ||
| resultList[['prot2rxn']] <- gdf | ||
| resultList[['metProteinCommonReactions']] <- data.frame() | ||
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| # find common reactions | ||
| if(nrow(mdf) > 0 && nrow(gdf) > 0) { | ||
| mRampRxnIds <- unlist(mdf$ramp_rxn_id) | ||
| gRampRxnIds <- unlist(gdf$ramp_rxn_id) | ||
| commonRxnIds <- intersect(mRampRxnIds, gRampRxnIds) | ||
| if(length(commonRxnIds) > 0) { | ||
| mRxn <- mdf[mdf$ramp_rxn_id %in% commonRxnIds,] | ||
| gRxn <- gdf[gdf$ramp_rxn_id %in% commonRxnIds,] | ||
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| # one row per reaction, include concat mets, concat proteins | ||
| # probably a more streamlined way to do this... | ||
| commonRampRxnList <- c() | ||
| commonRxnList <- c() | ||
| mRxnSourceIds <- c() | ||
| mRxnSourceNames <- c() | ||
| gRxnSourceIds <- c() | ||
| gRxnSourceName <- c() | ||
| gRxnUniprot <- c() | ||
| commonRxnLabel <- c() | ||
| commonRxnHTMLEq <- c() | ||
| hasHumanProtein <- c() | ||
| onlyHumanMets <- c() | ||
| isTransport <- c() | ||
| rxnDir <- c() | ||
| for(rxn in commonRxnIds) { | ||
| commonRampRxnList <- c(commonRampRxnList, rxn) | ||
| commonRxnList <- c(commonRxnList, paste0(unique(mRxn$rxn_source_id[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
| mRxnSourceIds <- c(mRxnSourceIds, paste0(unique(mRxn$sourceId[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
| mRxnSourceNames <- c(mRxnSourceNames, paste0(unique(mRxn$met_name[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
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| gRxnSourceIds <- c(gRxnSourceIds, paste0(unique(gRxn$sourceId[gRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
| gRxnUniprot <- c(gRxnUniprot, paste0(unique(gRxn$uniprot[gRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
| gRxnSourceName <- c(gRxnSourceName, paste0(unique(gRxn$protein_name[gRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
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| rxnDir <- c(rxnDir, paste0(unique(mRxn$direction[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
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| commonRxnLabel <- c(commonRxnLabel, paste0(unique(mRxn$label[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
| commonRxnHTMLEq <- c(commonRxnHTMLEq, paste0(unique(mRxn$html_equation[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
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| isTransport <- c(isTransport, paste0(unique(mRxn$is_transport[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
| hasHumanProtein <- c(hasHumanProtein, paste0(unique(mRxn$has_human_prot[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
| onlyHumanMets <- c(onlyHumanMets, paste0(unique(mRxn$only_human_mets[mRxn$ramp_rxn_id == rxn]), collapse = ',')) | ||
| } | ||
| commonReactions <- data.frame(list('metabolites' = mRxnSourceIds, 'met_names' = mRxnSourceNames ,'genes' = gRxnSourceIds, | ||
| 'uniprot' = gRxnUniprot, 'proteinNames' = gRxnSourceName, | ||
| 'reactionId' = commonRxnList, 'rxn_dir' = rxnDir,'rxn_label' = commonRxnLabel, | ||
| 'rxn_html_label' = commonRxnHTMLEq, | ||
| 'is_transport' = isTransport, | ||
| 'has_human_protein' = hasHumanProtein, | ||
| 'only_human_mets' = onlyHumanMets)) | ||
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| resultList[['metProteinCommonReactions']] <- commonReactions | ||
| } | ||
| } | ||
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| return(resultList) | ||
| } | ||
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| #' getReactionsForRaMPCompoundIds returns reactions for a collection of ramp compound ids | ||
| #' | ||
| #' @param rampCompoundIds list of ramp compound ids | ||
| #' @param onlyHumanMets boolean to only return pathways containing only human metabolites (ChEBI ontology) (dev in progress) | ||
| #' @param humanProtein boolean to only control pathways catalyzed by a human proteins (having human Uniprot) (dev in progress) | ||
| #' @param includeTransportRxns if TRUE, returns metabolic and transport reactions | ||
| #' | ||
| #' @return returns a dataframe of reaction information for each ramp compound id | ||
| getReactionsForRaMPCompoundIds <- function(rampCompoundIds, onlyHumanMets=F, humanProtein=F, includeTransportRxns=F, rxnDirs=c("UN")) { | ||
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| idStr <- listToQueryString(rampCompoundIds) | ||
| query <- paste0("select mr.ramp_rxn_id, mr.ramp_cmpd_id, mr.met_source_id, mr.substrate_product, mr.is_cofactor, mr.met_name, | ||
| mr.ramp_rxn_id, rxn.rxn_source_id, rxn.is_transport, rxn.label, rxn.direction, rxn.equation, rxn.html_equation, rxn.ec_num, rxn.has_human_prot, rxn.only_human_mets | ||
| from reaction2met mr, reaction rxn | ||
| where mr.ramp_cmpd_id in (",idStr,") and rxn.ramp_rxn_id = mr.ramp_rxn_id") | ||
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| if(length(rxnDirs) == 1) { | ||
| query <- paste0(query, " and rxn.direction = '",rxnDirs[1],"'") | ||
| } else if(length(rxnDirs)>1) { | ||
| query <- paste0(query, " and rxn.direction in (",listToQueryString(rxnDirs),")") | ||
| } else { | ||
| print("rxnDirs must be of length > 0") | ||
| } | ||
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| if(humanProtein) { | ||
| query <- paste0(query," and rxn.has_human_prot = 1") | ||
| } | ||
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| if(onlyHumanMets) { | ||
| query <- paste0(query, " and rxn.only_human_mets = 1") | ||
| } | ||
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| if(!includeTransportRxns) { | ||
| query <- paste0(query, " and rxn.is_transport = 0") | ||
| } | ||
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| conn <- connectToRaMP() | ||
| df <- RMariaDB::dbGetQuery(conn,query) | ||
| RMariaDB::dbDisconnect(conn=conn) | ||
| return(df) | ||
| } | ||
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| #' getReactionsForRaMPGeneIds returns reactions for a collection of ramp compound ids | ||
| #' | ||
| #' @param rampGeneIds list of ramp compound ids | ||
| #' @param onlyHumanMets boolean to only return pathways containing only human metabolites (ChEBI ontology) (dev in progress) | ||
| #' @param humanProtein boolean to only control pathways catalyzed by a human proteins (having human Uniprot) (dev in progress) | ||
| #' @param includeTransportRxns if TRUE, returns metabolic and transport reactions | ||
| #' | ||
| #' @return returns a dataframe of reaction information for each ramp compound id | ||
| getReactionsForRaMPGeneIds <- function(rampGeneIds, onlyHumanMets=F, humanProtein=F, includeTransportRxns=F, rxnDirs=c("UN")) { | ||
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| idStr <- listToQueryString(rampGeneIds) | ||
| query <- paste0("select gr.ramp_rxn_id, gr.ramp_gene_id, gr.uniprot, gr.protein_name, | ||
| gr.ramp_rxn_id, rxn.rxn_source_id, rxn.is_transport, rxn.label, rxn.direction, rxn.equation, rxn.html_equation, rxn.ec_num, rxn.has_human_prot, rxn.only_human_mets | ||
| from reaction2protein gr, reaction rxn | ||
| where gr.ramp_gene_id in (",idStr,") and rxn.ramp_rxn_id = gr.ramp_rxn_id") | ||
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| if(length(rxnDirs) == 1) { | ||
| query <- paste0(query, " and rxn.direction = '",rxnDirs[1],"'") | ||
| } else if(length(rxnDirs)>1) { | ||
| query <- paste0(query, " and rxn.direction in (",listToQueryString(rxnDirs),")") | ||
| } else { | ||
| print("rxnDirs must be of length > 0") | ||
| } | ||
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| if(humanProtein) { | ||
| query <- paste0(query, " and rxn.has_human_prot = 1") | ||
| } | ||
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| if(onlyHumanMets) { | ||
| query <- paste0(query, " and rxn.only_human_mets = 1") | ||
| } | ||
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| if(!includeTransportRxns) { | ||
| query <- paste0(query, " and rxn.is_transport = 0") | ||
| } | ||
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| conn <- connectToRaMP() | ||
| df <- RMariaDB::dbGetQuery(conn,query) | ||
| RMariaDB::dbDisconnect(conn=conn) | ||
| return(df) | ||
| } | ||
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| ##################################################### | ||
| ################################### | ||
| # | ||
| # general dev note... perhaps the functions below should be moved to rampQueryHelpers | ||
| # | ||
| ## | ||
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| #' getRampSourceInfoFromAnalyteIDs Utility method to extract source table information from analyte ids | ||
| #' | ||
| #' @param analytes list of analyte ids | ||
| #' | ||
| #' @return returns a dataframe of ramp analyte source information | ||
| getRampSourceInfoFromAnalyteIDs <- function(analytes) { | ||
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| analyteStr <- listToQueryString(analytes) | ||
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| query = paste("select distinct sourceId, rampId, geneOrCompound from source where sourceId in (",analyteStr,")") | ||
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| conn <- connectToRaMP() | ||
| df <- RMariaDB::dbGetQuery(conn,query) | ||
| RMariaDB::dbDisconnect(conn=conn) | ||
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| return(df) | ||
| } | ||
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| #' listToQueryString utility method to convert an id list to a comma separate string, with single quoted values. | ||
| #' | ||
| #' @param analytes list of analytes (can be names or ids) | ||
| #' | ||
| #' @return comma separated list of single quoted analyte ids or names | ||
| listToQueryString <- function(analytes) { | ||
| analyteStr <- paste0("'", paste0(analytes, collapse = "','"), "'", sep="") | ||
| return (analyteStr) | ||
| } |
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