From 5 spectra in the peak group only 2 are retained, and now flags for which ones are removed are present.
>
pa@av_spectra$1234
$av_intra
$av_intra$2
cl mz i snr rsd count total inPurity ra frac snr_pass_flag minfrac_pass_flag ra_pass_flag pass_flag
1 1 76.03936 260408.3 8.168558 NA 1 1 1 100.00000 1 TRUE TRUE TRUE TRUE
2 2 87.05532 146866.0 4.606933 NA 1 1 1 56.39836 1 TRUE TRUE TRUE TRUE
$av_intra$3
cl mz i snr rsd count total inPurity ra frac snr_pass_flag minfrac_pass_flag ra_pass_flag pass_flag
1 1 76.03939 387969.3 9.944705 53.27152 2 2 1 72.63818 1 TRUE TRUE TRUE TRUE
2 2 87.05528 275511.9 7.062117 24.43868 2 2 1 51.58316 1 TRUE TRUE TRUE TRUE
``
>
pa@grped_ms2$1234
[[1]]
[,1] [,2]
[1,] 50.01557 921.1038
[2,] 51.02344 1703.2170
[3,] 52.01890 863.3292
[4,] 58.06551 1357.3210
[5,] 62.01553 713.1802
[6,] 62.92937 22061.6680
[7,] 63.02336 928.4113
[8,] 63.92888 4076.4280
[9,] 64.18902 704.4742
[10,] 64.92747 1621.6434
[11,] 70.06499 933.9158
[12,] 74.09650 721.6017
[13,] 76.03937 4613.7686
[14,] 82.64358 701.4169
[15,] 87.05553 1146.8417
[16,] 89.03884 1021.0724
[17,] 90.92950 775.0679
[18,] 95.04922 1272.6851
[19,] 98.06015 1559.4219
[20,] 105.96336 1471.1497
[21,] 107.95026 1670.2163
[22,] 116.13265 731.6583
[23,] 121.96613 1027.8542
[24,] 125.28481 777.2943
[25,] 133.06065 1336.6599
[26,] 144.07999 723.9156
[27,] 149.99741 1323.1761
[28,] 150.23601 687.5054
[29,] 162.05566 759.3861
[30,] 167.02388 3471.1697
[31,] 178.73198 813.5861
[[2]]
[,1] [,2]
[1,] 50.01559 1283.4817
[2,] 51.02339 1680.2363
[3,] 51.22222 552.0405
[4,] 52.89830 605.9756
[5,] 58.06548 1588.9603
[6,] 61.54425 685.7117
[7,] 62.01529 842.8239
[8,] 62.12664 631.6484
[9,] 62.92934 27617.1602
[10,] 63.02320 1746.2920
[11,] 63.88893 615.5449
[12,] 63.92894 5638.6279
[13,] 64.92746 3266.7673
[14,] 65.03875 738.9711
[15,] 66.15918 677.6177
[16,] 70.06518 684.8496
[17,] 74.09651 1855.7240
[18,] 76.03940 4177.2236
[19,] 79.20387 613.4620
[20,] 87.05527 3352.0144
[21,] 89.03860 1753.1893
[22,] 98.06007 2796.7131
[23,] 105.96281 1392.4180
[24,] 107.95052 1219.4855
[25,] 108.90427 925.5315
[26,] 116.07047 1023.8954
[27,] 118.06483 884.3790
[28,] 121.96614 1048.5869
[29,] 123.98153 1197.1688
[30,] 135.69659 879.2622
[31,] 144.08060 1583.9188
[32,] 149.01352 1434.3975
[33,] 149.99742 1520.7753
[34,] 162.05470 1677.3496
[35,] 167.02385 1517.7867
[[3]]
[,1] [,2]
[1,] 57.89136 27293.72
[2,] 68.13218 29213.34
[3,] 76.03936 260408.34
[4,] 87.05532 146866.03
[5,] 101.84837 31550.03
[6,] 160.96516 32208.68
[[4]]
[,1] [,2]
[1,] 53.16459 60097.17
[2,] 76.03942 534112.06
[3,] 77.78919 92281.82
[4,] 87.05525 323122.44
[5,] 91.48993 69106.78
[6,] 101.85719 76224.40
[7,] 102.97038 77937.10
[8,] 133.06093 86291.38
[9,] 152.53438 78336.17
[[5]]
[,1] [,2]
[1,] 51.35890 30431.23
[2,] 56.07704 29754.07
[3,] 76.03936 241826.47
[4,] 76.43085 31852.93
[5,] 80.44976 34344.87
[6,] 82.04591 31178.42
[7,] 85.86448 29377.30
[8,] 87.05531 227901.34
[9,] 104.75587 37067.77
[10,] 112.30231 30200.48
[11,] 122.46079 35904.29
[12,] 144.23920 35326.61
[13,] 176.26358 34763.23
[14,] 202.34436 39012.65
``
pa@av_intra_params
$minfrac
[1] 0.5
$minnum
[1] 1
$ppm
[1] 5
$snr
[1] 0
$ra
[1] 0
$av
[1] "median"
$sum_i
[1] FALSE
$plim
[1] 0.8
$ra_pre
[1] 0
$snr_pre
[1] 3
$cores
[1] 3
$remove_peaks
[1] FALSE