hmdbconc can be installed directly from GitHub using the remotes package.
remotes::install_github('wilsontom/hmdbconc')To retrieve the "Normal Concentration" table for a single accession.
methyl_histidine <- hmdbconc::get_concentrations('0000001')
str(methyl_histidine)
tibble [49 × 9] (S3: tbl_df/tbl/data.frame)
$ name : chr [1:49] "1-Methylhistidine" "1-Methylhistidine" "1-Methylhistidine" "1-Methylhistidine" ...
$ accession : 'glue' chr [1:49] "HMDB0000001" "HMDB0000001" "HMDB0000001" "HMDB0000001" ...
$ biospecimen : chr [1:49] "Blood" "Blood" "Blood" "Blood" ...
$ concentration_value: chr [1:49] NA "7.7 +/- 1.9" "14.4 +/- 2.3" "19.6 +/- 2.6" ...
$ concentration_units: chr [1:49] NA "uM" "uM" "uM" ...
$ subject_age : chr [1:49] "Adult (>18 years old)" "Adult (>18 years old)" "Adult (>18 years old)" "Adult (>18 years old)" ...
$ subject_sex : chr [1:49] "Both" "Both" "Both" "Both" ...
$ subject_condition : chr [1:49] "Normal" "Normal" "Normal" "Normal" ...
$ pubmed : chr [1:49] "32966057" "7061274" "7061274" "7061274" ...
To iterate over multiple accessions and combine the results
accession_ids <- c('0000001', '0000002', '0000005')
concentration_tables <-
purrr::map(accession_ids, hmdbconc::get_concentrations) %>%
dplyr::bind_rows()
str(concentration_tables)
tibble [71 × 9] (S3: tbl_df/tbl/data.frame)
$ name : chr [1:71] "1-Methylhistidine" "1-Methylhistidine" "1-Methylhistidine" "1-Methylhistidine" ...
$ accession : 'glue' chr [1:71] "HMDB0000001" "HMDB0000001" "HMDB0000001" "HMDB0000001" ...
$ biospecimen : chr [1:71] "Blood" "Blood" "Blood" "Blood" ...
$ concentration_value: chr [1:71] NA "7.7 +/- 1.9" "14.4 +/- 2.3" "19.6 +/- 2.6" ...
$ concentration_units: chr [1:71] NA "uM" "uM" "uM" ...
$ subject_age : chr [1:71] "Adult (>18 years old)" "Adult (>18 years old)" "Adult (>18 years old)" "Adult (>18 years old)" ...
$ subject_sex : chr [1:71] "Both" "Both" "Both" "Both" ...
$ subject_condition : chr [1:71] "Normal" "Normal" "Normal" "Normal" ...
$ pubmed : chr [1:71] "32966057" "7061274" "7061274" "7061274" ...