Mercurial > repos > lain > xseeker
comparison resources/XSeeker/config/models.R @ 0:15c9fbefeaf1 draft
" master branch Updating"
author | lain |
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date | Tue, 01 Feb 2022 14:19:30 +0000 |
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-1:000000000000 | 0:15c9fbefeaf1 |
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1 | |
2 tryCatch({ | |
3 DBModelR::ModelDefinition(table="yui", fields=list(yui="INTEGER")) | |
4 }, error=function(e) { | |
5 stop("Please, install DBModelR before you source this file.") | |
6 }) | |
7 | |
8 list( | |
9 adduct=DBModelR::ModelDefinition( | |
10 table="adduct", | |
11 fields=list( | |
12 name="TEXT", | |
13 mass="FLOAT", | |
14 charge="INTEGER", | |
15 multi="INTEGER", | |
16 formula_add="TEXT", | |
17 formula_ded="TEXT", | |
18 sign="TEXT", | |
19 oidscore="INTEGER", | |
20 quasi="INTEGER", | |
21 ips="FLOAT" | |
22 ) | |
23 ), | |
24 cluster=DBModelR::ModelDefinition( | |
25 table="cluster", | |
26 fields=list( | |
27 clusterID="INTEGER", | |
28 formula="TEXT", | |
29 annotation="TEXT", | |
30 coeff="FLOAT", | |
31 r_squared="FLOAT", | |
32 charge="INTEGER", | |
33 mean_rt="FLOAT", | |
34 score="FLOAT", | |
35 deviation="FLOAT", | |
36 status="TEXT", | |
37 # adduct="TEXT", | |
38 curent_group="INTEGER", | |
39 pc_group="INTEGER", | |
40 align_group="INTEGER", | |
41 xcms_group="INTEGER" | |
42 ), | |
43 one=list("compound", "adduct"), | |
44 many=list("sample") | |
45 ), | |
46 compound=DBModelR::ModelDefinition( | |
47 table="compound", | |
48 fields=list( | |
49 name="TEXT", | |
50 common_name="TEXT", | |
51 formula="TEXT", | |
52 charge="INTEGER", | |
53 date="TEXT", | |
54 mz="FLOAT" | |
55 ) | |
56 ), | |
57 feature=DBModelR::ModelDefinition( | |
58 table="feature", | |
59 fields=list( | |
60 featureID="INTEGER", | |
61 mz="FLOAT", | |
62 mz_min="FLOAT", | |
63 mz_max="FLOAT", | |
64 rt="FLOAT", | |
65 rt_min="FLOAT", | |
66 rt_max="FLOAT", | |
67 int_o="FLOAT", | |
68 int_b="FLOAT", | |
69 max_o="FLOAT", | |
70 iso="TEXT", | |
71 abundance="FLOAT" | |
72 ), | |
73 one=list("cluster"), | |
74 many=list("sample") | |
75 ), | |
76 instrument=DBModelR::ModelDefinition( | |
77 table="instrument", | |
78 fields=list( | |
79 model="TEXT", | |
80 manufacturer="TEXT", | |
81 analyzer="TEXT", | |
82 detector_type="TEXT", | |
83 ion_source="TEXT" | |
84 ) | |
85 ), | |
86 instrument_config=DBModelR::ModelDefinition( | |
87 table="instrument_config", | |
88 fields=list( | |
89 resolution="TEXT", | |
90 agc_target="TEXT", | |
91 maximum_IT="TEXT", | |
92 number_of_scan_range="TEXT", | |
93 scan_range="TEXT", | |
94 version="TEXT" | |
95 ) | |
96 ), | |
97 project=DBModelR::ModelDefinition( | |
98 table="project", | |
99 fields=list( | |
100 name="TEXT", | |
101 comment="TEXT" | |
102 ), | |
103 one=list("sample") | |
104 ), | |
105 sample=DBModelR::ModelDefinition( | |
106 table="sample", | |
107 fields=list( | |
108 name="TEXT", | |
109 path="TEXT", | |
110 polarity="TEXT", | |
111 kind="TEXT", ## rdata or mxml or enriched_rdata | |
112 raw="BLOB" | |
113 ), | |
114 one=list( | |
115 "peak_picking_parameters", | |
116 "pairing_parameters", | |
117 "alignmenmt_parameters", | |
118 "camera_parameters", | |
119 "instrument", | |
120 "instrument_config", | |
121 "software", | |
122 "smol_xcms_set" | |
123 ) | |
124 ), | |
125 smol_xcms_set=DBModelR::ModelDefinition( | |
126 table="smol_xcms_set", | |
127 fields=list( | |
128 raw="BLOB" | |
129 ) | |
130 ), | |
131 software=DBModelR::ModelDefinition( | |
132 table="software", | |
133 fields=list( | |
134 name="TEXT", | |
135 version="TEXT" | |
136 ) | |
137 ), | |
138 # camera_parameters=DBModelR::ModelDefinition( | |
139 # table="camera_parameters", | |
140 # fields=list() | |
141 # ), | |
142 # pairing_parameters=DBModelR::ModelDefinition( | |
143 # table="pairing_parameters", | |
144 # fields=list() | |
145 # ), | |
146 peak_picking_parameters=DBModelR::ModelDefinition( | |
147 table="peak_picking_parameters", | |
148 fields=list( | |
149 ppm="FLOAT", | |
150 peakwidth="TEXT", | |
151 snthresh="TEXT", | |
152 prefilterStep="TEXT", | |
153 prefilterLevel="TEXT", | |
154 mzdiff="TEXT", | |
155 fitgauss="TEXT", | |
156 noise="TEXT", | |
157 mzCenterFun="TEXT", | |
158 integrate="INTEGER", | |
159 firstBaselineCheck="TEXT", | |
160 snthreshIsoROIs="TEXT", | |
161 maxCharge="INTEGER", | |
162 maxIso="INTEGER", | |
163 mzIntervalExtension="TEXT" | |
164 ) | |
165 ), | |
166 alignmenmt_parameters=DBModelR::ModelDefinition( | |
167 table="alignmenmt_parameters", | |
168 fields=list( | |
169 binSize="TEXT", | |
170 centerSample="TEXT", | |
171 response="TEXT", | |
172 distFun="TEXT", | |
173 gapInit="TEXT", | |
174 gapExtend="TEXT", | |
175 factorDiag="TEXT", | |
176 factorGap="TEXT", | |
177 localAlignment="INTEGER", | |
178 initPenalty="TEXT", | |
179 bw="TEXT", | |
180 minFraction="TEXT", | |
181 minSamples="TEXT", | |
182 maxFeatures="TEXT" | |
183 ) | |
184 ) | |
185 ) |