Read 'Agilent ChemStation' report files
Source:R/read_chemstation_report.R
read_chemstation_reports.RdReads peak tables from 'Agilent ChemStation' Report.TXT files, or from the
Result.xml files 'ChemStation' writes when set up to export its results.
Only Result.xml records where each peak starts and ends, so it is read in
preference to a Report.TXT in the same directory.
Arguments
- paths
Paths to 'ChemStation'
Report.TXTorResult.xmlfiles.- peaktable_format
Whether to return peak tables in the standard
chromatographrlayout (the default) or with all the columns the file provides (original). Achromatographrtable has the columnsrt,start,end,area,heightandFWHM(the full width at half maximum), with times in the same unit as the format's chromatograms andNAwhere the file does not record a value.- metadata_format
Format to output metadata. Either
chromconverterorraw.- data_format
Deprecated. Use
peaktable_formatinstead.
Value
A peak_list: a list with one element per report, named by its
.D directory, each holding one peak table per signal, named by
wavelength.
Examples
path <- system.file("extdata", "benzoxazinoid_standards", "BENZOS_250PPM.D",
"Report.TXT", package = "chromConverter")
read_chemstation_reports(path)
#> $BENZOS_250PPM
#> $BENZOS_250PPM$`254`
#> sample lambda rt start end area height FWHM
#> 1 BENZOS_250PPM 254 1.948 NA NA 140.95924 7.07890 0.2483
#> 2 BENZOS_250PPM 254 2.373 NA NA 161.74519 14.59622 0.1433
#> 3 BENZOS_250PPM 254 2.517 NA NA 108.11900 16.77651 0.0912
#> 4 BENZOS_250PPM 254 2.669 NA NA 102.54382 21.65732 0.0752
#> 5 BENZOS_250PPM 254 2.769 NA NA 389.25211 31.26716 0.1612
#> 6 BENZOS_250PPM 254 3.898 NA NA 1211.76770 18.42384 0.7973
#> 7 BENZOS_250PPM 254 5.063 NA NA 382.35251 11.64398 0.4211
#> 8 BENZOS_250PPM 254 5.319 NA NA 160.09975 10.35239 0.2244
#> 9 BENZOS_250PPM 254 5.615 NA NA 192.40610 9.96399 0.2633
#> 10 BENZOS_250PPM 254 6.108 NA NA 335.43140 9.27820 0.4398
#> 11 BENZOS_250PPM 254 6.621 NA NA 283.18048 7.90439 0.4360
#> 12 BENZOS_250PPM 254 7.223 NA NA 158.82758 6.81299 0.3060
#> 13 BENZOS_250PPM 254 7.916 NA NA 356.50873 5.75635 0.7946
#> 14 BENZOS_250PPM 254 12.541 NA NA 7078.15283 349.55142 0.3142
#> 15 BENZOS_250PPM 254 14.203 NA NA 136.62770 2.82697 0.6119
#> 16 BENZOS_250PPM 254 17.754 NA NA 78.47887 2.87611 0.4023
#> 17 BENZOS_250PPM 254 19.068 NA NA 10954.20000 456.22156 0.3721
#> 18 BENZOS_250PPM 254 20.979 NA NA 1806.64539 76.05057 0.3652
#> 19 BENZOS_250PPM 254 28.225 NA NA 637.83038 27.49332 0.3587
#> 20 BENZOS_250PPM 254 36.643 NA NA 61.25155 1.62191 0.5246
#>
#> $BENZOS_250PPM$`320`
#> sample lambda rt start end area height FWHM
#> 1 BENZOS_250PPM 320 2.370 NA NA 96.84458 11.83100 0.1115
#> 2 BENZOS_250PPM 320 2.502 NA NA 107.63147 16.68902 0.0992
#> 3 BENZOS_250PPM 320 2.664 NA NA 103.81037 22.40874 0.0740
#> 4 BENZOS_250PPM 320 2.763 NA NA 248.60339 29.45256 0.1165
#> 5 BENZOS_250PPM 320 3.881 NA NA 289.27115 6.79315 0.5888
#> 6 BENZOS_250PPM 320 5.066 NA NA 132.71829 5.38092 0.3278
#> 7 BENZOS_250PPM 320 5.602 NA NA 59.05860 3.18974 0.2620
#> 8 BENZOS_250PPM 320 12.508 NA NA 25.50664 1.10318 0.3397
#> 9 BENZOS_250PPM 320 14.201 NA NA 142.02574 3.56716 0.5565
#> 10 BENZOS_250PPM 320 19.066 NA NA 195.75963 8.10717 0.3617
#>
#> $BENZOS_250PPM$`360`
#> sample lambda rt start end area height FWHM
#> 1 BENZOS_250PPM 360 0.516 NA NA 96.44804 2.89953 0.4541
#> 2 BENZOS_250PPM 360 2.369 NA NA 574.00183 20.06062 0.3498
#> 3 BENZOS_250PPM 360 2.500 NA NA 131.14888 20.44745 0.0968
#> 4 BENZOS_250PPM 360 2.664 NA NA 126.34191 26.98949 0.0746
#> 5 BENZOS_250PPM 360 2.760 NA NA 392.27814 37.21136 0.1390
#> 6 BENZOS_250PPM 360 3.868 NA NA 1322.81958 20.69460 0.8197
#> 7 BENZOS_250PPM 360 5.070 NA NA 409.06174 12.16724 0.4322
#> 8 BENZOS_250PPM 360 5.600 NA NA 334.84705 10.31378 0.4008
#> 9 BENZOS_250PPM 360 6.622 NA NA 510.97223 7.16129 0.8464
#> 10 BENZOS_250PPM 360 14.216 NA NA 117.29733 2.52298 0.6144
#>
#> $BENZOS_250PPM$`210`
#> sample lambda rt start end area height FWHM
#> 1 BENZOS_250PPM 210 1.950 NA NA 65.69608 5.745110 0.1454
#> 2 BENZOS_250PPM 210 2.133 NA NA 84.84812 7.271900 0.1521
#> 3 BENZOS_250PPM 210 2.372 NA NA 70.46403 7.173740 0.1306
#> 4 BENZOS_250PPM 210 2.528 NA NA 52.72128 8.513370 0.0882
#> 5 BENZOS_250PPM 210 2.668 NA NA 51.72952 11.215840 0.0738
#> 6 BENZOS_250PPM 210 2.769 NA NA 165.68953 16.845010 0.1308
#> 7 BENZOS_250PPM 210 3.855 NA NA 291.84818 8.058200 0.4505
#> 8 BENZOS_250PPM 210 4.133 NA NA 114.18034 7.664050 0.1978
#> 9 BENZOS_250PPM 210 5.061 NA NA 169.26221 13.544000 0.1858
#> 10 BENZOS_250PPM 210 5.601 NA NA 54.17995 4.207650 0.1942
#> 11 BENZOS_250PPM 210 6.061 NA NA 288.09384 7.110250 0.5607
#> 12 BENZOS_250PPM 210 7.882 NA NA 244.28961 5.905900 0.5226
#> 13 BENZOS_250PPM 210 9.119 NA NA 399.80270 7.620720 0.6681
#> 14 BENZOS_250PPM 210 9.591 NA NA 178.11578 7.189960 0.3410
#> 15 BENZOS_250PPM 210 10.153 NA NA 394.09256 6.719370 0.7363
#> 16 BENZOS_250PPM 210 11.895 NA NA 171.44041 6.975670 0.3467
#> 17 BENZOS_250PPM 210 12.541 NA NA 19569.60000 952.719240 0.3196
#> 18 BENZOS_250PPM 210 14.184 NA NA 595.64838 16.776040 0.5262
#> 19 BENZOS_250PPM 210 15.338 NA NA 27.37215 1.095760 0.3234
#> 20 BENZOS_250PPM 210 17.748 NA NA 160.59375 6.482190 0.3970
#> 21 BENZOS_250PPM 210 19.069 NA NA 29204.10000 1202.623540 0.3793
#> 22 BENZOS_250PPM 210 20.978 NA NA 13595.20000 578.575740 0.3621
#> 23 BENZOS_250PPM 210 24.907 NA NA 42.35772 0.962402 0.5695
#> 24 BENZOS_250PPM 210 28.225 NA NA 13109.10000 560.928890 0.3647
#> 25 BENZOS_250PPM 210 36.622 NA NA 91.77909 3.710720 0.3766
#>
#> $BENZOS_250PPM$`230`
#> sample lambda rt start end area height FWHM
#> 1 BENZOS_250PPM 230 0.488 NA NA 68.80820 1.56110 0.5542
#> 2 BENZOS_250PPM 230 1.050 NA NA 220.37210 4.62333 0.5681
#> 3 BENZOS_250PPM 230 2.130 NA NA 276.37167 11.37646 0.3034
#> 4 BENZOS_250PPM 230 2.375 NA NA 143.48412 13.19617 0.1429
#> 5 BENZOS_250PPM 230 2.524 NA NA 93.12847 13.96627 0.1111
#> 6 BENZOS_250PPM 230 2.670 NA NA 76.98081 16.60342 0.0741
#> 7 BENZOS_250PPM 230 2.772 NA NA 376.92337 25.19552 0.1905
#> 8 BENZOS_250PPM 230 3.901 NA NA 1044.86316 15.04501 0.8662
#> 9 BENZOS_250PPM 230 5.063 NA NA 342.35373 11.03793 0.4019
#> 10 BENZOS_250PPM 230 5.600 NA NA 268.37524 9.23586 0.3790
#> 11 BENZOS_250PPM 230 6.079 NA NA 583.56812 10.26005 0.6996
#> 12 BENZOS_250PPM 230 7.892 NA NA 671.10590 8.78248 0.9595
#> 13 BENZOS_250PPM 230 9.124 NA NA 548.67072 8.08717 0.8355
#> 14 BENZOS_250PPM 230 9.593 NA NA 217.67584 7.66411 0.3794
#> 15 BENZOS_250PPM 230 10.164 NA NA 386.70090 7.08682 0.6846
#> 16 BENZOS_250PPM 230 11.278 NA NA 142.06198 5.90577 0.3126
#> 17 BENZOS_250PPM 230 12.541 NA NA 4126.13525 181.33946 0.3455
#> 18 BENZOS_250PPM 230 14.202 NA NA 438.22104 6.59593 0.8711
#> 19 BENZOS_250PPM 230 15.471 NA NA 82.90569 1.72794 0.5798
#> 20 BENZOS_250PPM 230 17.752 NA NA 40.14959 1.41113 0.3679
#> 21 BENZOS_250PPM 230 19.068 NA NA 5640.98242 235.13190 0.3759
#> 22 BENZOS_250PPM 230 20.978 NA NA 10423.30000 449.60464 0.3585
#> 23 BENZOS_250PPM 230 28.225 NA NA 11725.60000 505.16583 0.3628
#> 24 BENZOS_250PPM 230 36.660 NA NA 54.50668 1.01376 0.6673
#>
#> attr(,"instrument")
#> [1] "Instrument 1"
#> attr(,"detector")
#> [1] NA
#> attr(,"software")
#> [1] NA
#> attr(,"method")
#> [1] "ETHAN_DT_MEOH_L16-6.M"
#> attr(,"batch")
#> [1] NA
#> attr(,"operator")
#> [1] "Mario"
#> attr(,"run_datetime")
#> [1] "2023-06-21 16:46:40 UTC"
#> attr(,"sample_name")
#> [1] "benzos_250ppm"
#> attr(,"sample_injection_volume")
#> [1] 15
#> attr(,"sample_amount")
#> [1] NA
#> attr(,"time_range")
#> [1] NA
#> attr(,"time_interval")
#> [1] NA
#> attr(,"time_unit")
#> [1] NA
#> attr(,"detector_range")
#> [1] NA
#> attr(,"detector_y_unit")
#> [1] NA
#> attr(,"sample_injection_volume_unit")
#> [1] "µl"
#> attr(,"source_file")
#> [1] "/home/runner/work/_temp/Library/chromConverter/extdata/benzoxazinoid_standards/BENZOS_250PPM.D/Report.TXT"
#> attr(,"source_file_format")
#> [1] "chemstation_peaklist"
#> attr(,"source_sha1")
#> [1] "a896810f0154fa1183beedc4684f2b56ee00caca"
#> attr(,"format_out")
#> [1] "data.frame"
#> attr(,"data_format")
#> [1] "chromatographr"
#> attr(,"parser")
#> [1] NA
#>
#> attr(,"chrom_list")
#> [1] NA
#> attr(,"lambdas")
#> [1] "254" "320" "360" "210" "230"
#> attr(,"fit")
#> [1] "chemstation"
#> attr(,"sd.max")
#> [1] NA
#> attr(,"max.iter")
#> [1] NA
#> attr(,"time.units")
#> [1] "min"
#> attr(,"class")
#> [1] "peak_list"