To allow users to access data inside of reference databases without
causing lag, we opted to created reference databases as a Rcpp object.
This means that users are not able to access them unless you use the
get_reference_data() function.
To create a reference database object, you can either use the
read_msp() function or the read_hmdb()
function. Using the length() function will allow you to see
the amount of references.
reference_db <- read_msp(msp_file = mums2_example("massbank_example_data.msp"))
#> Reading: /home/runner/work/_temp/Library/mums2/extdata/massbank_example_data.msp ...
print(reference_db)
#> You have 8068 references in this object.
length(reference_db)
#> [1] 8068The get_reference_data() function will return the
reference at the specified index you input. This allows you to see the
data that is inside of your database.
get_reference_data(reference_db, 1)
#> $info
#> $info$keys
#> [1] "name" "precursormz" "precursortype" "formula"
#> [5] "ontology" "inchikey" "smiles" "retentiontime"
#> [9] "ccs" "ionmode" "instrumenttype" "instrument"
#> [13] "collisionenergy" "comment" "num peaks"
#>
#> $info$values
#> [1] "Veratramine; LC-ESI-TOF; MS2; CE\r"
#> [2] "410.305356\r"
#> [3] "[M+H]+\r"
#> [4] "C27H39NO2\r"
#> [5] "Fluorenes\r"
#> [6] "MALFODICFSIXPO-KFKQDBFTSA-N\r"
#> [7] "C[C@H]([C@@H]1NC[C@@H](C)C[C@H]1O)C1=C(C)C2=C(C=C1)[C@@H]1CC=C3C[C@@H](O)CC[C@]3(C)[C@H]1C2\r"
#> [8] "\r"
#> [9] "207.3842046\r"
#> [10] "Positive\r"
#> [11] "LC-ESI-QTOF\r"
#> [12] "\r"
#> [13] "\r"
#> [14] "registered in MassBank\r"
#> [15] "83\r"
#>
#>
#> $spec
#> $spec$mz
#> [1] 84.1 105.1 107.1 114.1 115.1 119.1 121.1 124.1 125.1 129.1 131.1 132.1
#> [13] 133.1 134.1 144.1 145.1 146.1 147.1 151.1 155.1 156.1 157.1 158.1 159.1
#> [25] 160.1 161.1 167.1 168.1 169.1 170.1 171.1 172.1 173.1 175.1 181.1 182.1
#> [37] 183.1 184.1 185.1 193.1 194.1 195.1 196.1 197.1 198.1 206.1 207.1 208.1
#> [49] 209.1 211.1 212.2 219.1 220.1 221.1 222.1 223.1 233.1 234.1 235.2 236.2
#> [61] 237.2 247.2 248.2 249.2 251.2 262.2 263.2 277.2 278.2 280.2 281.2 295.2
#> [73] 296.2 297.2 309.2 319.2 320.2 333.2 375.3 392.3 393.3 396.3 410.3
#>
#> $spec$intensity
#> [1] 32 6 6 105 7 8 6 83 8 7 129 13 212 23 5
#> [16] 108 12 14 8 26 17 372 45 216 29 6 6 7 121 17
#> [31] 350 47 10 5 27 12 108 18 18 16 6 37 12 41 7
#> [46] 8 28 8 23 51 9 6 11 35 13 11 16 8 34 13
#> [61] 12 16 18 17 6 42 11 77 17 17 22 1000 225 26 7
#> [76] 10 6 9 6 62 18 8 16
get_reference_data(reference_db, 2)
#> $info
#> $info$keys
#> [1] "name" "precursormz" "precursortype" "formula"
#> [5] "ontology" "inchikey" "smiles" "retentiontime"
#> [9] "ccs" "ionmode" "instrumenttype" "instrument"
#> [13] "collisionenergy" "comment" "num peaks"
#>
#> $info$values
#> [1] "Cyclopamine; LC-ESI-TOF; MS2; CE\r"
#> [2] "412.321006\r"
#> [3] "[M+H]+\r"
#> [4] "C27H41NO2\r"
#> [5] "Jerveratrum-type alkaloids\r"
#> [6] "QASFUMOKHFSJGL-LAFRSMQTSA-N\r"
#> [7] "C[C@@H]1[C@@H]2NC[C@@H](C)C[C@H]2O[C@]11CC[C@H]2[C@@H]3CC=C4C[C@@H](O)CC[C@]4(C)[C@H]3CC2=C1C\r"
#> [8] "\r"
#> [9] "207.2302643\r"
#> [10] "Positive\r"
#> [11] "LC-ESI-QTOF\r"
#> [12] "\r"
#> [13] "\r"
#> [14] "registered in MassBank\r"
#> [15] "99\r"
#>
#>
#> $spec
#> $spec$mz
#> [1] 67.1 81.1 84.1 85.1 93.1 96.1 102.1 105.1 107.1 109.1 110.1 112.1
#> [13] 114.1 115.1 119.1 121.1 124.1 125.1 126.1 127.1 129.1 131.1 133.1 134.1
#> [25] 135.1 140.1 143.1 144.1 145.1 146.1 147.1 148.1 149.1 150.1 151.1 155.1
#> [37] 156.1 157.1 158.1 159.1 160.1 161.1 162.1 163.1 167.1 169.1 170.1 171.1
#> [49] 172.1 173.1 174.1 175.1 177.1 181.1 182.1 183.1 184.1 185.1 186.1 187.1
#> [61] 195.1 196.1 197.1 198.1 199.1 200.2 201.2 207.1 209.1 210.1 211.1 212.2
#> [73] 213.2 214.2 221.1 222.1 223.1 224.2 225.2 227.2 235.1 237.2 239.2 249.2
#> [85] 251.2 253.2 264.2 269.2 279.2 280.2 281.2 287.2 295.2 297.2 321.2 322.2
#> [97] 377.3 394.3 412.3
#>
#> $spec$intensity
#> [1] 29 47 87 70 30 30 68 52 82 724 62 53 693 41 110
#> [16] 94 50 27 295 25 32 151 607 60 149 185 277 45 889 99
#> [31] 271 31 48 46 76 107 55 1000 132 860 104 334 37 80 24
#> [46] 162 37 566 82 330 43 57 26 58 38 218 60 244 37 76
#> [61] 140 56 254 47 138 28 26 29 113 35 174 28 352 53 31
#> [76] 28 79 25 61 27 43 71 62 30 58 79 27 28 100 28
#> [91] 35 42 58 43 130 38 44 55 113The combined_reference_database() function allows you to
combined two different databases ontop of eachother to make one
reference database.
reference_db_2 <-
read_msp(msp_file = mums2_example("massbank_example_data_negative.msp"))
#> Reading: /home/runner/work/_temp/Library/mums2/extdata/massbank_example_data_negative.msp ...
length(reference_db_2)
#> [1] 4782
combined_db <- combined_reference_database(reference_db, reference_db_2)
length(combined_db)
#> [1] 12850