## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse=TRUE, comment="#>", warning=FALSE, error=FALSE, eval=FALSE ) ## ----library, message=FALSE, warning=FALSE, error=FALSE----------------------- # library(BiocStyle) # library(HPAanalyze) # library(dplyr) # library(jsonlite) ## ----------------------------------------------------------------------------- # data <- hpaDownload(downloadList = "histology", version = "example") # data_subset <- # hpaSubset(data, # targetGene = c('TP53', 'EGFR', 'CD44', 'PTEN', 'IDH1')) ## ----------------------------------------------------------------------------- # data_json <- lapply(data_subset, jsonlite::toJSON) # # str(data_json) # # # List of 3 # # $ normal_tissue : 'json' chr "[{\"ensembl\":\"ENSG00000026508\",\"gene\":\"CD44\",\"tissue\":\"adrenal gland\",\"cell_type\":\"glandular cell"| __truncated__ # # $ pathology : 'json' chr "[{\"ensembl\":\"ENSG00000026508\",\"gene\":\"CD44\",\"cancer\":\"breast cancer\",\"high\":1,\"medium\":6,\"low\"| __truncated__ # # $ subcellular_location: 'json' chr "[{\"ensembl\":\"ENSG00000026508\",\"gene\":\"CD44\",\"reliability\":\"Enhanced\",\"enhanced\":\"Golgi apparatus"| __truncated__ ## ----------------------------------------------------------------------------- # for (i in seq_along(data_json)) { # write(data_json[[i]], # file = paste0("hpa_data_", names(data_json[i]), ".json")) # } ## ----------------------------------------------------------------------------- # ## The function (note that you don't need to put .json into the file name) # hpaExportJSON <- function(data, fileName) { # data_json <- lapply(data, jsonlite::toJSON) # for (i in seq_along(data_json)) { # write(data_json[[i]], # file = paste0(fileName, "_", names(data_json[i]), ".json")) # } # } # # ## Export data subset # hpaExportJSON(data_subset, fileName = "hpa_data")