This function will change your ms1 peak table rt time to
rt time in seconds or minutes. This modification happens in place
(or by reference), so the mpactr_object will be updated.
Arguments
- mpactr_object
The object created from
import_all_data()file.- rt_type
how you want to convert your retention time, your options are minutes, or seconds. defaults to seconds.
Examples
data <-
import_all_data(peak_table =
mums2::mums2_example("botryllus_pt_small.csv"),
meta_data =
mums2::mums2_example("meta_data_boryillus.csv"),
format = "None")
#> If peak table has corrupted compound names they will be converted to
#> utf-8 and if there are any commas, they will be converted to periods(.).
change_rt_to_seconds_or_minute(data, "minutes")
#> [1] "Changing rt values to minutes"
#> Compound mz RTINMINUTES 221012_DGM_Blank1_1_1_390
#> <char> <num> <num> <num>
#> 1: 413.12834 Da 319.32 s 414.1356 0.08866667 1643.672
#> 2: 655.22101 Da 481.62 s 656.2283 0.13383333 0.000
#> 3: 904.69182 Da 604.24 s 905.6991 0.16783333 0.000
#> 4: 798.49680 Da 604.00 s 799.5041 0.16783333 6537.559
#> 5: 641.41035 Da 429.52 s 642.4176 0.11933333 0.000
#> ---
#> 1496: 575.41282 Da 489.35 s 576.4201 0.13600000 29761.977
#> 1497: 338.24828 Da 464.42 s 339.2556 0.12900000 0.000
#> 1498: 620.35620 Da 402.49 s 621.3635 0.11183333 0.000
#> 1499: 329.31242 Da 367.23 s 330.3197 0.10200000 27427.938
#> 1500: 922.75982 Da 516.14 s 905.7584 0.14333333 10774.994
#> 221012_DGM_Blank1_1_2_391 221012_DGM_Blank1_1_3_392
#> <num> <num>
#> 1: 1683.589 1581.715
#> 2: 0.000 0.000
#> 3: 0.000 4459.532
#> 4: 0.000 0.000
#> 5: 0.000 0.000
#> ---
#> 1496: 25043.342 29393.545
#> 1497: 0.000 0.000
#> 1498: 0.000 0.000
#> 1499: 0.000 27899.057
#> 1500: 9953.737 0.000
#> 221012_DGM_MB1588_3_1_395 221012_DGM_MB1588_3_2_396
#> <num> <num>
#> 1: 0.000 1842.961
#> 2: 0.000 0.000
#> 3: 0.000 0.000
#> 4: 0.000 0.000
#> 5: 0.000 0.000
#> ---
#> 1496: 21414.033 16893.291
#> 1497: 0.000 0.000
#> 1498: 0.000 0.000
#> 1499: 8513.641 9216.000
#> 1500: 20867.770 22925.033
#> 221012_DGM_MB1588_3_3_397 221012_DGM_MB1589_4_1_398
#> <num> <num>
#> 1: 0.000 1540.177
#> 2: 8839.863 0.000
#> 3: 4535.730 0.000
#> 4: 0.000 8426.455
#> 5: 0.000 0.000
#> ---
#> 1496: 9563.822 19355.344
#> 1497: 2631.964 24679.939
#> 1498: 0.000 0.000
#> 1499: 8127.656 0.000
#> 1500: 8899.025 0.000
#> 221012_DGM_MB1589_4_2_399 221012_DGM_MB1589_4_3_400
#> <num> <num>
#> 1: 1379.541 1349.259
#> 2: 0.000 8058.202
#> 3: 0.000 4271.522
#> 4: 11090.130 7521.545
#> 5: 0.000 15678.532
#> ---
#> 1496: 23032.473 17940.416
#> 1497: 30655.693 26387.342
#> 1498: 0.000 0.000
#> 1499: 6196.938 10507.124
#> 1500: 8226.452 0.000
#> 221012_DGM_MB1590_5_1_401 221012_DGM_MB1590_5_2_402
#> <num> <num>
#> 1: 1736.740 1674.615
#> 2: 0.000 0.000
#> 3: 0.000 0.000
#> 4: 13776.298 8939.586
#> 5: 15058.773 16887.570
#> ---
#> 1496: 21241.809 19027.691
#> 1497: 4935.798 0.000
#> 1498: 0.000 0.000
#> 1499: 8340.333 8436.562
#> 1500: 12247.824 13145.450
#> 221012_DGM_MB1590_5_3_403 221012_DGM_Blank2_1_1_404
#> <num> <num>
#> 1: 0.000 1661.673
#> 2: 0.000 16815.256
#> 3: 0.000 0.000
#> 4: 0.000 5920.994
#> 5: 15524.373 0.000
#> ---
#> 1496: 25560.471 18392.838
#> 1497: 3977.483 1765.111
#> 1498: 0.000 0.000
#> 1499: 9480.690 0.000
#> 1500: 23735.074 15348.451
#> 221012_DGM_Blank2_1_2_405 221012_DGM_Blank2_1_3_406
#> <num> <num>
#> 1: 2047.95 1189.160
#> 2: 17501.14 5604.232
#> 3: 0.00 0.000
#> 4: 0.00 3559.699
#> 5: 0.00 0.000
#> ---
#> 1496: 25072.64 20801.066
#> 1497: 0.00 0.000
#> 1498: 0.00 0.000
#> 1499: 0.00 0.000
#> 1500: 14027.31 6547.833
#> 221012_DGM_MB1591_6_1_407 221012_DGM_MB1591_6_2_408
#> <num> <num>
#> 1: 1573.228 0.000
#> 2: 0.000 0.000
#> 3: 2709.508 2182.018
#> 4: 5700.309 2390.115
#> 5: 0.000 0.000
#> ---
#> 1496: 17008.381 21820.496
#> 1497: 1779.258 3069.007
#> 1498: 0.000 3495.131
#> 1499: 8185.514 8341.350
#> 1500: 0.000 0.000
#> 221012_DGM_MB1591_6_3_409 221012_DGM_MB1592_7_1_410
#> <num> <num>
#> 1: 1092.180 1813.853
#> 2: 6107.080 2540.801
#> 3: 0.000 0.000
#> 4: 5241.544 0.000
#> 5: 13128.431 0.000
#> ---
#> 1496: 11963.309 3578.613
#> 1497: 0.000 62719.613
#> 1498: 0.000 0.000
#> 1499: 10087.337 31680.289
#> 1500: 0.000 0.000
#> 221012_DGM_MB1592_7_2_411 221012_DGM_MB1592_7_3_412
#> <num> <num>
#> 1: 1505.633 1203.859
#> 2: 2162.738 11592.640
#> 3: 2738.020 0.000
#> 4: 0.000 3995.891
#> 5: 0.000 0.000
#> ---
#> 1496: 4033.957 8272.763
#> 1497: 57441.410 54402.375
#> 1498: 9849.991 10114.544
#> 1499: 46649.805 39742.734
#> 1500: 0.000 0.000
#> 221012_DGM_MB1593_8_1_413 221012_DGM_MB1593_8_2_414
#> <num> <num>
#> 1: 1327.427 1740.172
#> 2: 0.000 4208.383
#> 3: 0.000 0.000
#> 4: 5239.572 7006.156
#> 5: 16500.930 0.000
#> ---
#> 1496: 11067.920 13218.476
#> 1497: 8315.789 6651.864
#> 1498: 0.000 0.000
#> 1499: 0.000 20481.836
#> 1500: 0.000 0.000
#> 221012_DGM_MB1593_8_3_415 221012_DGM_MB1594_9_1_416
#> <num> <num>
#> 1: 1380.644 1635.196
#> 2: 7293.763 0.000
#> 3: 0.000 3350.652
#> 4: 8872.400 3247.472
#> 5: 0.000 0.000
#> ---
#> 1496: 21657.127 16811.928
#> 1497: 8297.395 48881.785
#> 1498: 0.000 6538.799
#> 1499: 24633.131 29117.193
#> 1500: 0.000 0.000
#> 221012_DGM_MB1594_9_2_417 221012_DGM_MB1594_9_3_418
#> <num> <num>
#> 1: 1337.972 1377.6218
#> 2: 0.000 7568.2002
#> 3: 0.000 0.0000
#> 4: 7382.616 0.0000
#> 5: 0.000 0.0000
#> ---
#> 1496: 16662.057 8798.4893
#> 1497: 53517.762 51970.5234
#> 1498: 9830.620 0.0000
#> 1499: 0.000 37141.7617
#> 1500: 0.000 519.6837
#> 221012_DGM_Blank3_1_1_419 221012_DGM_Blank3_1_2_420
#> <num> <num>
#> 1: 1256.6434 1920.330
#> 2: 10593.5996 0.000
#> 3: 0.0000 5863.393
#> 4: 0.0000 0.000
#> 5: 0.0000 0.000
#> ---
#> 1496: 9507.4121 0.000
#> 1497: 0.0000 0.000
#> 1498: 0.0000 0.000
#> 1499: 0.0000 0.000
#> 1500: 465.6117 0.000
#> 221012_DGM_Blank3_1_3_421 221012_DGM_MB1595_10_1_422
#> <num> <num>
#> 1: 1438.921 1270.993
#> 2: 8887.850 3453.785
#> 3: 0.000 3040.876
#> 4: 3100.021 0.000
#> 5: 0.000 0.000
#> ---
#> 1496: 8573.043 0.000
#> 1497: 0.000 115468.789
#> 1498: 0.000 0.000
#> 1499: 0.000 15698.000
#> 1500: 0.000 0.000
#> 221012_DGM_MB1595_10_2_423 221012_DGM_MB1595_10_3_424
#> <num> <num>
#> 1: 1232.581 1769.550
#> 2: 2805.313 3917.201
#> 3: 0.000 3773.011
#> 4: 3969.096 3393.127
#> 5: 0.000 0.000
#> ---
#> 1496: 5298.672 5166.771
#> 1497: 116873.945 113807.047
#> 1498: 0.000 0.000
#> 1499: 13476.294 0.000
#> 1500: 0.000 0.000
#> 221012_DGM_MB1597_11_1_425 221012_DGM_MB1597_11_2_426
#> <num> <num>
#> 1: 1469.424 1916.736
#> 2: 0.000 5492.965
#> 3: 1994.700 0.000
#> 4: 0.000 7475.469
#> 5: 0.000 0.000
#> ---
#> 1496: 8280.562 11125.481
#> 1497: 1513.106 0.000
#> 1498: 0.000 0.000
#> 1499: 7428.072 8648.967
#> 1500: 0.000 0.000
#> 221012_DGM_MB1597_11_3_427 221012_DGM_MB1598_12_1_428
#> <num> <num>
#> 1: 2275.196 0.0000
#> 2: 3876.187 0.0000
#> 3: 0.000 0.0000
#> 4: 8617.719 0.0000
#> 5: 0.000 0.0000
#> ---
#> 1496: 9527.089 8534.1504
#> 1497: 3575.851 84401.3516
#> 1498: 0.000 16802.7012
#> 1499: 9848.295 13961.7207
#> 1500: 0.000 712.7478
#> 221012_DGM_MB1598_12_2_429 221012_DGM_MB1598_12_3_430
#> <num> <num>
#> 1: 1318.5538 0.000
#> 2: 0.0000 6346.356
#> 3: 0.0000 5324.371
#> 4: 0.0000 3165.401
#> 5: 0.0000 0.000
#> ---
#> 1496: 8152.6548 0.000
#> 1497: 0.0000 0.000
#> 1498: 10476.6221 11861.588
#> 1499: 0.0000 0.000
#> 1500: 437.0028 0.000
#> 221012_DGM_MB1599_13_1_431 221012_DGM_MB1599_13_2_432
#> <num> <num>
#> 1: 1066.136 0.000
#> 2: 6197.055 13562.388
#> 3: 6451.301 4927.146
#> 4: 2199.003 0.000
#> 5: 0.000 0.000
#> ---
#> 1496: 11158.275 15178.959
#> 1497: 2599.609 2878.922
#> 1498: 7530.887 0.000
#> 1499: 11578.348 11530.500
#> 1500: 0.000 0.000
#> 221012_DGM_MB1599_13_3_433 221012_DGM_Blank4_1_1_434
#> <num> <num>
#> 1: 966.0234 1861.986
#> 2: 32407.8379 15096.834
#> 3: 5301.7993 0.000
#> 4: 2455.8958 2673.542
#> 5: 0.0000 13200.256
#> ---
#> 1496: 13624.2832 14405.179
#> 1497: 0.0000 0.000
#> 1498: 0.0000 0.000
#> 1499: 9885.8184 0.000
#> 1500: 0.0000 0.000
#> 221012_DGM_Blank4_1_2_435 221012_DGM_Blank4_1_3_436 kmd
#> <num> <num> <num>
#> 1: 1202.606 1478.475 0.13562
#> 2: 24745.084 15284.740 0.22829
#> 3: 508.500 0.000 0.69910
#> 4: 4999.417 3814.854 0.50408
#> 5: 0.000 0.000 0.41763
#> ---
#> 1496: 13660.577 13074.628 0.42010
#> 1497: 0.000 0.000 0.25556
#> 1498: 0.000 0.000 0.36347
#> 1499: 20086.701 0.000 0.31970
#> 1500: 0.000 0.000 0.75836