How to convert information in a JSON file into a dataframe in R?

I have some information in the JSON file named data.json like below:

{
  "header" : {
    "apiVersion" : "v1",
    "code" : "200",
    "service" : "catalogwebservice",
    "developerMessage" : "",
    "userMessage" : "OK",
    "errorCode" : "1",
    "docLink" : "https://ega-archive.org",
    "errorStack" : ""
  },
  "response" : {
    "numTotalResults" : 12,
    "resultType" : "SampleData",
    "result" : [ {
      "alias" : "JKDFG093.T2",
      "egaStableId" : "EGAN00003456789",
      "centerName" : "Novartis",
      "creationTime" : "2016-05-13Y17:08.001Z",
      "title" : "JKDFG093.T2",
      "bioSampleId" : "MADFG110656789",
      "subjectId" : "JKDFG093",
      "gender" : "male",
      "phenotype" : "Cancer",
      "attributes" : null
    }, {
      "alias" : "JKDFG093.T1",
      "egaStableId" : "EGAN00003456780",
      "centerName" : "Novartis",
      "creationTime" : "2016-05-13Y17:08.001Z",
      "title" : "JKDFG093.T1",
      "bioSampleId" : "MADFG110656790",
      "subjectId" : "JKDFG093",
      "gender" : "female",
      "phenotype" : "Cancer",
      "attributes" : null
    }, {
      "alias" : "JKDFG087.T1",
      "egaStableId" : "EGAN00003456781",
      "centerName" : "Novartis",
      "creationTime" : "2016-05-13Y17:08.001Z",
      "title" : "JKDFG087.T1",
      "bioSampleId" : "MADFG110656791",
      "subjectId" : "JKDFG087",
      "gender" : "male",
      "phenotype" : "Cancer",
      "attributes" : null
    } ]
  }
}

I want to convert the information in a JSON file into a data frame. I need information like alias, egaStableId, centerName, creationTime, title, bioSampleId, subjectId, gender, phenotype, and attributes from the above JSON file as column names and their respective information showing in the data frame.

I loaded the JSON file in R and tried converting it into a data frame, but ended up with some errors.

library(rjson)
data <- rjson::fromJSON(file = "data.json")
json_data_frame <- as.data.frame(data)

The error I got:

Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE,  : 
  arguments imply differing number of rows: 1, 0

Any help is appreciated. Thank you !!

You need to dig into the data to get to the results, namely $response$result.

Replace json here with your filename:

jsonlite::fromJSON(json)$response$result
#         alias     egaStableId centerName          creationTime       title    bioSampleId subjectId gender phenotype attributes
# 1 JKDFG093.T2 EGAN00003456789   Novartis 2016-05-13Y17:08.001Z JKDFG093.T2 MADFG110656789  JKDFG093   male    Cancer         NA
# 2 JKDFG093.T1 EGAN00003456780   Novartis 2016-05-13Y17:08.001Z JKDFG093.T1 MADFG110656790  JKDFG093 female    Cancer         NA
# 3 JKDFG087.T1 EGAN00003456781   Novartis 2016-05-13Y17:08.001Z JKDFG087.T1 MADFG110656791  JKDFG087   male    Cancer         NA

Namely, if you look at the output from fromJSON, you'll see that there is a frame nested (a little deeply) in the list:

str(jsonlite::fromJSON(json))
# List of 2
#  $ header  :List of 8
#   ..$ apiVersion      : chr "v1"
#   ..$ code            : chr "200"
#   ..$ service         : chr "catalogwebservice"
#   ..$ developerMessage: chr ""
#   ..$ userMessage     : chr "OK"
#   ..$ errorCode       : chr "1"
#   ..$ docLink         : chr "https://ega-archive.org"
#   ..$ errorStack      : chr ""
#  $ response:List of 3
#   ..$ numTotalResults: int 12
#   ..$ resultType     : chr "SampleData"
#   ..$ result         :'data.frame':	3 obs. of  10 variables:
#   .. ..$ alias       : chr [1:3] "JKDFG093.T2" "JKDFG093.T1" "JKDFG087.T1"
#   .. ..$ egaStableId : chr [1:3] "EGAN00003456789" "EGAN00003456780" "EGAN00003456781"
#   .. ..$ centerName  : chr [1:3] "Novartis" "Novartis" "Novartis"
#   .. ..$ creationTime: chr [1:3] "2016-05-13Y17:08.001Z" "2016-05-13Y17:08.001Z" "2016-05-13Y17:08.001Z"
#   .. ..$ title       : chr [1:3] "JKDFG093.T2" "JKDFG093.T1" "JKDFG087.T1"
#   .. ..$ bioSampleId : chr [1:3] "MADFG110656789" "MADFG110656790" "MADFG110656791"
#   .. ..$ subjectId   : chr [1:3] "JKDFG093" "JKDFG093" "JKDFG087"
#   .. ..$ gender      : chr [1:3] "male" "female" "male"
#   .. ..$ phenotype   : chr [1:3] "Cancer" "Cancer" "Cancer"
#   .. ..$ attributes  : logi [1:3] NA NA NA

I'm using jsonlite, I believe it is close enough to rjson that the same thing should work. If yours is not listed as

  ..$ result         :'data.frame':	3 obs. of  10 variables:

in the str-output, then just wrap it in as.data.frame, as in

as.data.frame(jsonlite::fromJSON(json)$response$result)