Mercurial > repos > lain > xseeker

comparison resources/XSeeker/config/models.R @ 0:15c9fbefeaf1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
" master branch Updating"
author lain
date Tue, 01 Feb 2022 14:19:30 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:15c9fbefeaf1
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 )