## ----libraryLoad, warning=FALSE------------------------------------------ suppressMessages(library(ENCODExplorer)) ## ----query_results, collapse=TRUE---------------------------------------- query_results <- queryEncode(assay = "RNA-seq", organism = "Homo sapiens", biosample = "MCF-7", file_format = "fastq", fixed = TRUE) ## ----query_results_2, collapse=TRUE-------------------------------------- query_results <- queryEncode(assay = "rnaseq", organism = "Homo sapiens", biosample = "MCF-7", file_format = "fastq", fixed = TRUE) ## ----query_results_3, collapse=TRUE-------------------------------------- query_results <- queryEncode(assay = "rnaseq", organism = "Homo sapiens", biosample = "MCF-7", file_format = "fastq", fixed = FALSE) ## ----files, collapse=TRUE------------------------------------------------ related_files <- resolveEncodeAccession(accession = 'ENCSR918FQM') related_files$files ## ----search_results, collapse=TRUE--------------------------------------- search_results <- searchEncode(searchTerm = "a549 chip-seq homo sapiens", limit = "all") ## ----query_results_4, collapse=TRUE-------------------------------------- query_results <- queryEncode(assay = "switchgear", target ="elavl1", fixed = FALSE) ## ----search_results_2, collapse=TRUE------------------------------------- search_results <- searchEncode(searchTerm = "switchgear elavl1", limit = "all") ## ----query_results_5, collapse=TRUE, eval=TRUE--------------------------- query_results <- queryEncode(assay = "switchgear", target ="elavl1", file_format = "bed" , fixed = FALSE) downloadEncode(resultSet = query_results, resultOrigin = "queryEncode") ## ----collapse=TRUE, eval=TRUE-------------------------------------------- downloadEncode(resultSet = search_results, resultOrigin = "searchEncode", format = "bed") ## ----search_results_3, collapse=TRUE------------------------------------- search_results <- searchEncode(searchTerm = "switchgear elavl1", limit = "all") ## ----conert_results_1, collapse=TRUE------------------------------------- convert_results <- searchToquery(searchResults = search_results)