expandMzIntensity() expands a data.frame with m/z and/or intensity
values stored as a list in columns "mz" and "intensity". The resulting
data.frame has the m/z and intensity values stored as numeric in columns
"mz" and "intensity", one value per row, with the content of other
columns repeated as many times as there are m/z and intensity values.
Arguments
- x
data.framewith collapsed m/z and intensity values in columns"mz"and"intensity", such as returned bymsms_spectra_hmdb()with parametercollapsed = TRUE, or byspectraorcompoundscalls.
Examples
## Read a data.frame with collapsed columns mz and intensity columns
dr <- system.file("xml/", package = "CompoundDb")
msms_spctra <- msms_spectra_hmdb(dr)
#> Going to process 4 xml files.
#> Postprocessing data ...
#> OK
msms_spctra
#> original_spectrum_id compound_id polarity collision_energy predicted
#> 1 1 HMDB0000001 1 10 FALSE
#> 2 2 HMDB0000001 1 25 FALSE
#> 3 446575 HMDB0004370 1 NA FALSE
#> 4 370739 HMDB0006719 0 20 TRUE
#> splash instrument_type
#> 1 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 2 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 3 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 4 splash10-001i-0009000000-c16445787a057993951a <NA>
#> instrument precursor_mz mz intensity
#> 1 <NA> NA 109.2, 1.... 3.406999....
#> 2 <NA> NA 83.1, 96.... 6.685028....
#> 3 API3000, Applied Biosystems NA 44.1, 57.... 0.051124....
#> 4 <NA> NA 111.0815.... 0.550973....
#> spectrum_id
#> 1 1
#> 2 2
#> 3 3
#> 4 4
## Columns mz and intensity are "collased"
msms_spctra$mz
#> [[1]]
#> [1] 109.20 124.20 124.50 170.16 170.52
#>
#> [[2]]
#> [1] 83.10 96.12 97.14 109.14 124.08 125.10 170.16
#>
#> [[3]]
#> [1] 44.1 57.9 61.4 71.2 73.8 78.3 78.8 83.1 88.2 98.8 101.7 102.8
#> [13] 106.8 111.6 115.1 116.9 118.1 121.0 124.9 126.7 127.2 128.9 129.9 131.9
#> [25] 139.0 140.4 141.2 142.9 144.1 157.6 158.0 175.2 193.2
#>
#> [[4]]
#> [1] 111.0815 249.2588 273.2588 341.2850 353.3214 355.3006 355.3370 365.3214
#> [9] 367.3006 383.3319
#>
## Expand the data.frame to get one row per m/z and intensity value
spctra_exp <- expandMzIntensity(msms_spctra)
spctra_exp
#> original_spectrum_id compound_id polarity collision_energy predicted
#> 1 1 HMDB0000001 1 10 FALSE
#> 2 1 HMDB0000001 1 10 FALSE
#> 3 1 HMDB0000001 1 10 FALSE
#> 4 1 HMDB0000001 1 10 FALSE
#> 5 1 HMDB0000001 1 10 FALSE
#> 6 2 HMDB0000001 1 25 FALSE
#> 7 2 HMDB0000001 1 25 FALSE
#> 8 2 HMDB0000001 1 25 FALSE
#> 9 2 HMDB0000001 1 25 FALSE
#> 10 2 HMDB0000001 1 25 FALSE
#> 11 2 HMDB0000001 1 25 FALSE
#> 12 2 HMDB0000001 1 25 FALSE
#> 13 446575 HMDB0004370 1 NA FALSE
#> 14 446575 HMDB0004370 1 NA FALSE
#> 15 446575 HMDB0004370 1 NA FALSE
#> 16 446575 HMDB0004370 1 NA FALSE
#> 17 446575 HMDB0004370 1 NA FALSE
#> 18 446575 HMDB0004370 1 NA FALSE
#> 19 446575 HMDB0004370 1 NA FALSE
#> 20 446575 HMDB0004370 1 NA FALSE
#> 21 446575 HMDB0004370 1 NA FALSE
#> 22 446575 HMDB0004370 1 NA FALSE
#> 23 446575 HMDB0004370 1 NA FALSE
#> 24 446575 HMDB0004370 1 NA FALSE
#> 25 446575 HMDB0004370 1 NA FALSE
#> 26 446575 HMDB0004370 1 NA FALSE
#> 27 446575 HMDB0004370 1 NA FALSE
#> 28 446575 HMDB0004370 1 NA FALSE
#> 29 446575 HMDB0004370 1 NA FALSE
#> 30 446575 HMDB0004370 1 NA FALSE
#> 31 446575 HMDB0004370 1 NA FALSE
#> 32 446575 HMDB0004370 1 NA FALSE
#> 33 446575 HMDB0004370 1 NA FALSE
#> 34 446575 HMDB0004370 1 NA FALSE
#> 35 446575 HMDB0004370 1 NA FALSE
#> 36 446575 HMDB0004370 1 NA FALSE
#> 37 446575 HMDB0004370 1 NA FALSE
#> 38 446575 HMDB0004370 1 NA FALSE
#> 39 446575 HMDB0004370 1 NA FALSE
#> 40 446575 HMDB0004370 1 NA FALSE
#> 41 446575 HMDB0004370 1 NA FALSE
#> 42 446575 HMDB0004370 1 NA FALSE
#> 43 446575 HMDB0004370 1 NA FALSE
#> 44 446575 HMDB0004370 1 NA FALSE
#> 45 446575 HMDB0004370 1 NA FALSE
#> 46 370739 HMDB0006719 0 20 TRUE
#> 47 370739 HMDB0006719 0 20 TRUE
#> 48 370739 HMDB0006719 0 20 TRUE
#> 49 370739 HMDB0006719 0 20 TRUE
#> 50 370739 HMDB0006719 0 20 TRUE
#> 51 370739 HMDB0006719 0 20 TRUE
#> 52 370739 HMDB0006719 0 20 TRUE
#> 53 370739 HMDB0006719 0 20 TRUE
#> 54 370739 HMDB0006719 0 20 TRUE
#> 55 370739 HMDB0006719 0 20 TRUE
#> splash instrument_type
#> 1 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 2 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 3 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 4 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 5 splash10-00di-0900000000-037d24a7d65676b7e356 Quattro_QQQ
#> 6 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 7 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 8 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 9 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 10 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 11 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 12 splash10-00di-0900000000-03e99316bd6c098f5d11 Quattro_QQQ
#> 13 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 14 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 15 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 16 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 17 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 18 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 19 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 20 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 21 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 22 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 23 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 24 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 25 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 26 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 27 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 28 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 29 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 30 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 31 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 32 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 33 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 34 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 35 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 36 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 37 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 38 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 39 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 40 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 41 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 42 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 43 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 44 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 45 splash10-004i-0900000000-9f3d3580f44ff890d948 LC-ESI-QQ
#> 46 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 47 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 48 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 49 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 50 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 51 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 52 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 53 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 54 splash10-001i-0009000000-c16445787a057993951a <NA>
#> 55 splash10-001i-0009000000-c16445787a057993951a <NA>
#> instrument precursor_mz mz intensity spectrum_id
#> 1 <NA> NA 109.2000 3.4069998 1
#> 2 <NA> NA 124.2000 47.4945731 1
#> 3 <NA> NA 124.5000 3.0943658 1
#> 4 <NA> NA 170.1600 100.0000000 1
#> 5 <NA> NA 170.5200 13.2396932 1
#> 6 <NA> NA 83.1000 6.6850283 2
#> 7 <NA> NA 96.1200 4.3812987 2
#> 8 <NA> NA 97.1400 3.0221439 2
#> 9 <NA> NA 109.1400 16.7082568 2
#> 10 <NA> NA 124.0800 100.0000000 2
#> 11 <NA> NA 125.1000 4.5651409 2
#> 12 <NA> NA 170.1600 40.6434125 2
#> 13 API3000, Applied Biosystems NA 44.1000 0.0511240 3
#> 14 API3000, Applied Biosystems NA 57.9000 0.0065970 3
#> 15 API3000, Applied Biosystems NA 61.4000 0.0120940 3
#> 16 API3000, Applied Biosystems NA 71.2000 0.0016490 3
#> 17 API3000, Applied Biosystems NA 73.8000 0.0032980 3
#> 18 API3000, Applied Biosystems NA 78.3000 0.0060470 3
#> 19 API3000, Applied Biosystems NA 78.8000 0.0049480 3
#> 20 API3000, Applied Biosystems NA 83.1000 0.0153920 3
#> 21 API3000, Applied Biosystems NA 88.2000 0.0038480 3
#> 22 API3000, Applied Biosystems NA 98.8000 0.0087960 3
#> 23 API3000, Applied Biosystems NA 101.7000 0.0038480 3
#> 24 API3000, Applied Biosystems NA 102.8000 0.0021990 3
#> 25 API3000, Applied Biosystems NA 106.8000 0.0109940 3
#> 26 API3000, Applied Biosystems NA 111.6000 0.0038480 3
#> 27 API3000, Applied Biosystems NA 115.1000 0.1016990 3
#> 28 API3000, Applied Biosystems NA 116.9000 0.0555220 3
#> 29 API3000, Applied Biosystems NA 118.1000 0.4254850 3
#> 30 API3000, Applied Biosystems NA 121.0000 0.0082460 3
#> 31 API3000, Applied Biosystems NA 124.9000 0.0087960 3
#> 32 API3000, Applied Biosystems NA 126.7000 0.0032980 3
#> 33 API3000, Applied Biosystems NA 127.2000 0.0115440 3
#> 34 API3000, Applied Biosystems NA 128.9000 0.0038480 3
#> 35 API3000, Applied Biosystems NA 129.9000 0.0164920 3
#> 36 API3000, Applied Biosystems NA 131.9000 8.9527790 3
#> 37 API3000, Applied Biosystems NA 139.0000 0.0241880 3
#> 38 API3000, Applied Biosystems NA 140.4000 0.0115440 3
#> 39 API3000, Applied Biosystems NA 141.2000 0.0588200 3
#> 40 API3000, Applied Biosystems NA 142.9000 0.0571710 3
#> 41 API3000, Applied Biosystems NA 144.1000 36.3817270 3
#> 42 API3000, Applied Biosystems NA 157.6000 0.0357320 3
#> 43 API3000, Applied Biosystems NA 158.0000 0.3848060 3
#> 44 API3000, Applied Biosystems NA 175.2000 100.0000000 3
#> 45 API3000, Applied Biosystems NA 193.2000 0.0087960 3
#> 46 <NA> NA 111.0815 0.5509733 4
#> 47 <NA> NA 249.2588 0.7330056 4
#> 48 <NA> NA 273.2588 0.5171464 4
#> 49 <NA> NA 341.2850 0.6527944 4
#> 50 <NA> NA 353.3214 0.8764642 4
#> 51 <NA> NA 355.3006 0.7582467 4
#> 52 <NA> NA 355.3370 0.4985064 4
#> 53 <NA> NA 365.3214 21.2824831 4
#> 54 <NA> NA 367.3006 2.4354476 4
#> 55 <NA> NA 383.3319 52.1357554 4