## ----libraryLoad, message=FALSE, warning=FALSE----------------------------- library(ENCODExplorer) ## ----load_encodeDF, collapse=TRUE------------------------------------------ encode_df <- get_encode_df() ## ----query_results, collapse=TRUE, eval =T--------------------------------- query_results <- queryEncode(organism = "Homo sapiens", biosample_name = "MCF-7", file_format = "fastq", fixed = TRUE) ## ----query_results_2, collapse=TRUE---------------------------------------- query_results <- queryEncode(organism = "Homo sapiens", biosample_name = "mcf7", file_format = "fastq", fixed = TRUE, fuzzy = FALSE) ## ----query_results_3, collapse=TRUE---------------------------------------- query_results <- queryEncode(organism = "Homo sapiens", biosample_name = "mcf7", file_format = "fastq", fixed = TRUE, fuzzy = TRUE) ## ----query_results_4, collapse=TRUE---------------------------------------- query_results <- queryEncode(assay = ".*RNA-seq", biosample_name = "HeLa-S3", fixed = FALSE) table(query_results$assay) ## ----query_results_5, collapse=TRUE---------------------------------------- query_results <- queryEncodeGeneric(biosample_name="HeLa-S3", assay="RNA-seq", submitted_by="Diane Trout", fuzzy=TRUE) table(query_results$submitted_by) ## ----fuzzy_results, collapse=TRUE------------------------------------------ fuzzy_results <- fuzzySearch(searchTerm = c("brca")) ## ----fuzzy_results_2, collapse=TRUE---------------------------------------- fuzzy_results <- fuzzySearch(searchTerm = c("brca", "ZNF24"), filterVector = c("target"), multipleTerm = TRUE) ## ----search_results, collapse=TRUE----------------------------------------- search_results <- searchEncode(searchTerm = "a549 chip-seq homo sapiens", limit = "all") ## ----query_results_6, collapse=TRUE---------------------------------------- query_results <- queryEncode(assay = "switchgear", target ="elavl1", fixed = FALSE) ## ----search_results_1, collapse=TRUE--------------------------------------- search_results <- searchEncode(searchTerm = "switchgear elavl1", limit = "all") ## ----query_results_7, collapse=TRUE, eval=FALSE---------------------------- # query_results <- queryEncode(assay = "switchgear", target ="elavl1", # file_format = "bed" , fixed = FALSE) # downloadEncode(query_results) ## ----collapse=TRUE, eval=FALSE--------------------------------------------- # downloadEncode(search_results, format = "bed") ## ----search_results_2, collapse=TRUE--------------------------------------- search_results <- searchEncode(searchTerm = "switchgear elavl1", limit = "all") ## ----convert_results_1, collapse=TRUE-------------------------------------- convert_results <- searchToquery(searchResults = search_results) ## ----ah, message=FALSE----------------------------------------------------- require(AnnotationHub) ah = AnnotationHub() query(ah, "ENCODExplorerData")