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How to Use JBQR

JBQR is an R wrapper for JBQ, designed to simplify common functions and make them easier to use.

Create an Instance of the JBQ class

The constructor of the JBQ class accepts one parameter: the path to the data package directory or the zip file. This path can be either an absolute path or a relative path where the R script is executed.

# use zip file
# Replace 'path_to_zip_file' with the actual path where JAXDP00006X.zip is saved
jbq_obj <- JBQ$new("path_to_zip_file/JAXDP00006X.zip")

# use unzipped directory
# the full path for the data package folder, eg, `/tmp/JAXDP00006X`
jbq_obj <- JBQ$new("full_path_to_data_package_directory")

Show Study

Show all studies in a data package 

full_data_package_path <- "C:\\Users\\liangh\\Desktop\\BioConnect_Data\\JAXDP00006X"

jbq_obj <- JBQ$new(full_data_package_path)
jbq_obj$show_studies()
output 
 [1] ""                                                                                 
 [2] "Data Package Root: \"C:\\Users\\liangh\\Desktop\\BioConnect_Data\\JAXDP00006X\""  
 [3] "Read Sucess:  C:\\Users\\liangh\\Desktop\\BioConnect_Data\\JAXDP00006X"           
 [4] "  total number of triples: 3215"                                                  
 [5] ""                                                                                 
 [6] " Study"                                                                           
 [7] "+-- Name: JAXST00001R"                                                            
 [8] "+-- Title: Mass Spectrometry analysis of \"Three Bears\" mice on control or high "
 [9] "|   fat high sugar diet. Proteomics and Metabolomics."                            
[10] "+-- Description:  Starting at 6 weeks of age, half the animals per strain were "  
[11] "|   fed control diet, and the other half were fed high fat, high sugar diet "     
[12] "|   (HFHS). The same animals were used in metabolic phenotyping and RNA "         
[13] "|   sequencing."                                                                  
[14] "`-- Comments: "                                                                   
[15] "    `-- Species: mouse"

Get Assay Samples

Get all samples of the assays in a data package into a dataframe 

assay_samples = jbq_obj$get_assay_samples()
assay_samples
output 
> assay_samples
     sample_name                          source_name            diet    sex    strain treatment genotype
1   ORSAM17290-1 JMUSf37118ffca35cf6d2939ae5f8c941d14 10% fat + fiber female  C57BL/6J        NA       NA
2   ORSAM17291-1 JMUSe85c53436f70930c804c17124f048e32 10% fat + fiber female  C57BL/6J        NA       NA
3   ORSAM17292-1 JMUSbbaa0055849bba97849f0067c458e889 10% fat + fiber   male  C57BL/6J        NA       NA
4   ORSAM17293-1 JMUSc2113932b206a2c9749d1ad9d20655dd 10% fat + fiber   male  C57BL/6J        NA       NA
5   ORSAM17294-1 JMUS613846554fc300089758a7a2fe624f41 10% fat + fiber female NZO/HlLtJ        NA       NA
......
To avoid the line wrap for a table row, use options("width"=200) to set the terminal width

Show Files

Show all the files in a data package 

jbq_obj$show_files()
output 
> jbq_obj$show_files()
 [5] "                                     Files                                     "
 [6] "+-----------------------------------------------------------------------------+"
 [7] "| File Name                                    || Investi\x85 | Study   |Assay|"
 [8] "|----------------------------------------------++----------+---------+--------|"
 [9] "| 202111_CUBE_Islet_Discovery_Proteomics_ \x85 || JAXIN00\x85 | JAXST0\x85 | JAXAS\x85 |"
[10] "| 2021_CUBE_Adipose_C18negative_All-Data.xlsx  || JAXIN00\x85 | JAXST0\x85 | JAXAS\x85 |"
[11] "| 2021_CUBE_Adipose_C18negative_metadata.csv   || JAXIN00\x85 | JAXST0\x85 | JAXAS\x85 |"
[12] "| 2021_CUBE_Adipose_C18positive_All-Data.xlsx  || JAXIN00\x85 | JAXST0\x85 | JAXAS\x85 |"
[13] "| 2021_CUBE_Adipose_C18positive_metadata.csv   || JAXIN00\x85 | JAXST0\x85 | JAXAS\x85 |"
......

Download Files

Download files in a data package The file_names parameter in your command can accept either a single file name or a list of file names separated by commas.

You can use the wildcard * in the file_names parameter to match multiple files based on patterns.

  • at the beginning: Matches files ending with a specific suffix.
  • at the end: Matches files starting with a specific prefix.
  • at both ends: Matches files containing a specific substring.

The following will get download all the files whose file name contains "raw" 

jbq_obj$get_files("*liver*")
output

[8] " 10 Files, 124.0 MB to be downloaded"
 [9] "+-- 2021_CUBE_Liver_C18negative_All-Data.xlsx  20.7 MB"
[10] "+-- 2021_CUBE_Liver_C18negative_metadata.csv  3.9 KB"
[11] "+-- 2021_CUBE_Liver_C18positive_All-Data.xlsx  28.9 MB"
[12] "+-- 2021_CUBE_Liver_C18positive_metadata.csv  3.9 KB"
[13] "+-- 2021_CUBE_Liver_Discovery_Proteomics_Data.xlsx  58.8 MB"
[14] "+-- 2021_CUBE_Liver_HILICnegative_All-Data.xlsx  5.5 MB"
[15] "+-- 2021_CUBE_Liver_HILICnegative_metadata.csv  3.9 KB"
[16] "+-- 2021_CUBE_Liver_HILICpositive_All-Data.xlsx  9.9 MB"
[17] "+-- 2021_CUBE_Liver_HILICpositive_metadata.csv  3.9 KB"
[18] "`-- liver_metadata.csv  3.9 KB"
[19] "  1 saved: JAXDP00006X\\2021_CUBE_Liver_C18negative_All-Data.xlsx"
[20] "  2 saved: JAXDP00006X\\2021_CUBE_Liver_C18negative_metadata.csv"
[21] "  3 saved: JAXDP00006X\\2021_CUBE_Liver_C18positive_All-Data.xlsx"
[22] "  4 saved: JAXDP00006X\\2021_CUBE_Liver_C18positive_metadata.csv"
[23] "  5 saved: JAXDP00006X\\2021_CUBE_Liver_Discovery_Proteomics_Data.xlsx"
[24] "  6 saved: JAXDP00006X\\2021_CUBE_Liver_HILICnegative_All-Data.xlsx"
[25] "  7 saved: JAXDP00006X\\2021_CUBE_Liver_HILICnegative_metadata.csv"
[26] "  8 saved: JAXDP00006X\\2021_CUBE_Liver_HILICpositive_All-Data.xlsx"
[27] "  9 saved: JAXDP00006X\\2021_CUBE_Liver_HILICpositive_metadata.csv"
[28] "  10 saved: JAXDP00006X\\liver_metadata.csv"