### R code from vignette source 'IdMappingRetrieval.Rnw' ### Encoding: UTF-8 ################################################### ### code chunk number 1: chunk1 (eval = FALSE) ################################################### ## library(IdMappingRetrieval) ## # setup verbosity level,array type and DB keys ## arrayType <- "HG-U133_Plus_2"; ## primaryKey <- "Uniprot"; ## secondaryKey <- "Affy"; ## #initialize caching directory structure ## Annotation$init(directory="./annotationData",verbose=TRUE); ## #set Affymetrix credentials ## AnnotationAffx$setCredentials( ## user="alex.lisovich@gmail.com",password="125438",verbose=TRUE); ################################################### ### code chunk number 2: chunk2 (eval = FALSE) ################################################### ## #create Affymetrix service object ## annAffx_Q <- tryCatch( ## AnnotationAffx(cacheFolderName="Affymetrix", ## primaryColumn="Probe.Set.ID", ## secondaryColumn="SwissProt", ## swap=TRUE) ); ## #create Ensembl file-based service object ## annEnsemblCsv <- tryCatch( ## AnnotationEnsemblCsv( ## cacheFolderName="EnsemblCsv", ## primaryColumn=c("UniProt.SwissProt.Accession", ## "UniProt.TrEMBL.Accession"), ## secondaryColumn=NA, ## swap=FALSE, full.merge=TRUE, ## df_filename="ENSEMBL_biomart_export.txt") ); ## #create Envision service object ## annEnvision <- tryCatch( ## AnnotationEnvision( ## cacheFolderName="EnVision", ## primaryColumn=c("UniProt.SwissProt.Accession", ## "UniProt.TrEMBL.Accession"), ## secondaryColumn=NA, ## swap=TRUE, species="Homo sapiens", full.merge=TRUE) ); ## errorSummary = sapply(c('annAffx_Q', 'annEnsemblCsv', ''), function(service) ## inherits(service, "error") ) ## errorMesg = ifelse(any(errorSummary), ## paste("(In this vignette build, the service(s) ", ## names(which(errorSummary)), "timed out.)"), ## errorMesg = "(All services were successfully retrieved.)" ## ) ################################################### ### code chunk number 3: chunk3a (eval = FALSE) ################################################### ## # create service objects ## services <- list(); ## services$NetAffx_F <- AnnotationAffx("Affymetrix"); ## ## #collect Id Map data ## idMapList <- lapply(services, getIdMap, ## arrayType=arrayType, ## primaryKey=primaryKey, ## secondaryKey=secondaryKey, ## force=FALSE, verbose=TRUE); ## ################################################### ### code chunk number 4: chunk3b (eval = FALSE) ################################################### ## ## idMapList <- lapply(services, getIdMap, ## arrayType=arrayType, ## primaryKey=primaryKey, ## secondaryKey=secondaryKey, ## force=FALSE, verbose=TRUE); ## names(idMapList); ## idMapList$NetAffx_F[100:110,]; ################################################### ### code chunk number 5: chunk3c (eval = FALSE) ################################################### ## #collect complete data frames ## dfList <- lapply(services, getDataFrame, ## arrayType=arrayType, ## force=FALSE, verbose=TRUE); ## names(dfList); ## names(dfList$NetAffx_F); ################################################### ### code chunk number 6: chunk4 (eval = FALSE) ################################################### ## #create service manager object containing set of default services ## svm <- ServiceManager(ServiceManager$getDefaultServices()); ## names(getServices(svm)); ## idMapList <- getIdMapList(svm, ## arrayType=arrayType, ## selection=c("NetAffx_Q"), ## primaryKey=primaryKey, ## secondaryKey=secondaryKey, verbose=TRUE); ## #collect complete data frames ## dfList <- getDataFrameList(svm, ## arrayType=arrayType, ## selection=c("NetAffx_Q"), verbose=TRUE); ################################################### ### code chunk number 7: chunk5 (eval = FALSE) ################################################### ## #collect complete IdMap data interactively ## #selecting array type and services to collect data from ## idMapList <- ServiceManager$getIdMapList( ## primaryKey= primaryKey, ## secondaryKey=secondaryKey,verbose=TRUE); ## #collect complete data frames interactively ## #selecting array type and services to collect data from ## dfList <- ServiceManager$getDataFrameList( ## arrayType="menu", ## selection="menu", verbose=TRUE); ################################################### ### code chunk number 8: chunk6 (eval = FALSE) ################################################### ## #remove caching directory to prevent including it into tar.gz during build ## unlink("./annotationData",recursive=TRUE); ################################################### ### code chunk number 9: sessionInfo ################################################### toLatex(sessionInfo())