Takes an input object and returns a score table for the decoys.
decoyScoreTable(object, decoy, score, log10 = TRUE)A data.frame, mzID or mzRident object.
character, name of the variable that indicates if the peptide
matches to a target or to a decoy. When this value is missing, a Shiny
gadget is launched to select it interactively.
numeric, indicating the score of the peptide match, obtained
by the search engine. When this value is missing, a Shiny gadget is
launched to select it interactively.
logical to indicate if the score should be
-log10-transformed. Default: TRUE. When this value is missing, a Shiny
gadget is launched to select it interactively.
A data.frame with a logical "decoy" column and numeric "scores".
library(mzID)
## Use one of the example files in the mzID package
exampleFile <- system.file("extdata", "55merge_tandem.mzid", package = "mzID")
mzIDexample <- mzID(exampleFile)
#> reading 55merge_tandem.mzid... DONE!
decoyScoreTable(mzIDexample, decoy = "isdecoy", score = "x\\!tandem:expect")
#> decoy score
#> 1 FALSE 3.76955108
#> 2 FALSE 2.53760200
#> 3 FALSE 2.52287875
#> 4 FALSE 2.29242982
#> 5 FALSE 1.79588002
#> 6 TRUE 1.17392520
#> 7 TRUE 1.00000000
#> 8 TRUE 0.88605665
#> 9 TRUE 0.79588002
#> 10 TRUE 0.76955108
#> 11 TRUE 0.74472749
#> 12 TRUE 0.65757732
#> 13 TRUE 0.60205999
#> 14 FALSE 0.58502665
#> 15 TRUE 0.56863624
#> 16 TRUE 0.48148606
#> 17 TRUE 0.45593196
#> 18 TRUE 0.45593196
#> 19 FALSE 0.45593196
#> 20 FALSE 0.43179828
#> 21 TRUE 0.38721614
#> 22 TRUE 0.37675071
#> 23 TRUE 0.36653154
#> 24 TRUE 0.33724217
#> 25 TRUE 0.29242982
#> 26 TRUE 0.29242982
#> 27 TRUE 0.26760624
#> 28 TRUE 0.25963731
#> 29 FALSE 0.25963731
#> 30 FALSE 0.24412514
#> 31 TRUE 0.19382003
#> 32 TRUE 0.19382003
#> 33 TRUE 0.18708664
#> 34 TRUE 0.14874165
#> 35 TRUE 0.13667714
#> 36 FALSE 0.10790540
#> 37 TRUE 0.10237291
#> 38 TRUE 0.08092191
#> 39 TRUE 0.04575749
#> 40 TRUE 0.04575749
#> 41 TRUE 0.03151705
#> 42 TRUE 0.01322827
#> 43 FALSE -0.04139269
#> 44 TRUE -0.04139269
#> 45 TRUE -0.04139269
#> 46 TRUE -0.04139269
#> 47 TRUE -0.04139269
#> 48 TRUE -0.04139269
#> 49 TRUE -0.04139269
#> 50 FALSE -0.04139269
#> 51 FALSE -0.07918125
#> 52 FALSE -0.07918125
#> 53 TRUE -0.07918125
#> 54 TRUE -0.07918125
#> 55 TRUE -0.07918125
#> 56 FALSE -0.07918125
#> 57 TRUE -0.07918125
#> 58 TRUE -0.07918125
#> 59 FALSE -0.07918125
#> 60 FALSE -0.11394335
#> 61 TRUE -0.11394335
#> 62 TRUE -0.11394335
#> 63 TRUE -0.11394335
#> 64 FALSE -0.11394335
#> 65 TRUE -0.11394335
#> 66 TRUE -0.14612804
#> 67 TRUE -0.14612804
#> 68 TRUE -0.14612804
#> 69 TRUE -0.14612804
#> 70 TRUE -0.17609126
#> 71 TRUE -0.17609126
#> 72 TRUE -0.17609126
#> 73 TRUE -0.17609126
#> 74 TRUE -0.20411998
#> 75 TRUE -0.20411998
#> 76 TRUE -0.23044892
#> 77 FALSE -0.25527251
#> 78 TRUE -0.25527251
#> 79 FALSE -0.27875360
#> 80 TRUE -0.27875360
#> 81 FALSE -0.27875360
#> 82 TRUE -0.30103000
#> 83 FALSE -0.30103000
#> 84 TRUE -0.32221929
#> 85 TRUE -0.32221929
#> 86 FALSE -0.34242268
#> 87 TRUE -0.34242268
#> 88 TRUE -0.34242268
#> 89 FALSE -0.34242268
#> 90 TRUE -0.34242268
#> 91 TRUE -0.34242268
#> 92 TRUE -0.36172784
#> 93 TRUE -0.36172784
#> 94 FALSE -0.36172784
#> 95 FALSE -0.36172784
#> 96 FALSE -0.38021124
#> 97 TRUE -0.38021124
#> 98 TRUE -0.38021124
#> 99 TRUE -0.38021124
#> 100 TRUE -0.39794001
#> 101 TRUE -0.39794001
#> 102 TRUE -0.41497335
#> 103 FALSE -0.41497335
#> 104 TRUE -0.41497335
#> 105 TRUE -0.41497335
#> 106 FALSE -0.43136376
#> 107 TRUE -0.43136376
#> 108 TRUE -0.44715803
#> 109 FALSE -0.44715803
#> 110 TRUE -0.46239800
#> 111 TRUE -0.46239800
#> 112 TRUE -0.46239800
#> 113 TRUE -0.47712125
#> 114 TRUE -0.47712125
#> 115 TRUE -0.47712125
#> 116 TRUE -0.49136169
#> 117 TRUE -0.49136169
#> 118 TRUE -0.50514998
#> 119 TRUE -0.53147892
#> 120 FALSE -0.53147892
#> 121 TRUE -0.53147892
#> 122 FALSE -0.54406804
#> 123 TRUE -0.54406804
#> 124 FALSE -0.55630250
#> 125 FALSE -0.55630250
#> 126 TRUE -0.56820172
#> 127 FALSE -0.56820172
#> 127.1 TRUE -0.56820172
#> 128 TRUE -0.57978360
#> 129 TRUE -0.59106461
#> 130 FALSE -0.60205999
#> 130.1 FALSE -0.60205999
#> 131 TRUE -0.61278386
#> 132 TRUE -0.61278386
#> 133 TRUE -0.62324929
#> 134 FALSE -0.62324929
#> 135 TRUE -0.63346846
#> 136 TRUE -0.65321251
#> 137 TRUE -0.65321251
#> 138 TRUE -0.66275783
#> 139 TRUE -0.67209786
#> 140 FALSE -0.67209786
#> 141 FALSE -0.69019608
#> 142 TRUE -0.69019608
#> 143 TRUE -0.69897000
#> 144 TRUE -0.69897000
#> 145 TRUE -0.70757018
#> 146 FALSE -0.72427587
#> 147 TRUE -0.72427587
#> 148 TRUE -0.73239376
#> 149 TRUE -0.74818803
#> 150 TRUE -0.74818803
#> 151 FALSE -0.77085201
#> 152 TRUE -0.77815125
#> 153 TRUE -0.77815125
#> 154 TRUE -0.78532984
#> 155 TRUE -0.79934055
#> 156 FALSE -0.80617997
#> 157 TRUE -0.80617997
#> 158 FALSE -0.81291336
#> 159 TRUE -0.81291336
#> 160 TRUE -0.81954394
#> 161 TRUE -0.83884909
#> 162 TRUE -0.83884909
#> 163 FALSE -0.84509804
#> 164 TRUE -0.84509804
#> 165 TRUE -0.85733250
#> 166 FALSE -0.86923172
#> 167 TRUE -0.88081359
#> 168 TRUE -0.89762709
#> 169 TRUE -0.97312785