Mercurial > repos > fgiacomoni > xseekerpreparator

comparison data/models.R @ 0:1660665c081e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
#issue9 branch Updating - - Fxx
author fgiacomoni
date Thu, 19 Nov 2020 14:28:46 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:1660665c081e
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("sample", "compound")
44 ),
45 compound=DBModelR::ModelDefinition(
46 table="compound",
47 fields=list(
48 name="TEXT",
49 common_name="TEXT",
50 formula="TEXT",
51 charge="INTEGER",
52 date="TEXT",
53 mz="FLOAT"
54 )
55 ),
56 feature=DBModelR::ModelDefinition(
57 table="feature",
58 fields=list(
59 featureID="INTEGER",
60 mz="FLOAT",
61 mz_min="FLOAT",
62 mz_max="FLOAT",
63 rt="FLOAT",
64 rt_min="FLOAT",
65 rt_max="FLOAT",
66 int_o="FLOAT",
67 int_b="FLOAT",
68 max_o="FLOAT",
69 iso="TEXT",
70 abundance="FLOAT"
71 ),
72 one=list("cluster")
73 ),
74 instrument=DBModelR::ModelDefinition(
75 table="instrument",
76 fields=list(
77 model="TEXT",
78 manufacturer="TEXT",
79 analyzer="TEXT",
80 detector_type="TEXT",
81 ion_source="TEXT"
82 )
83 ),
84 instrument_config=DBModelR::ModelDefinition(
85 table="instrument_config",
86 fields=list(
87 resolution="TEXT",
88 agc_target="TEXT",
89 maximum_IT="TEXT",
90 number_of_scan_range="TEXT",
91 scan_range="TEXT",
92 version="TEXT"
93 )
94 ),
95 project=DBModelR::ModelDefinition(
96 table="project",
97 fields=list(
98 name="TEXT",
99 comment="TEXT"
100 ),
101 one=list("sample")
102 ),
103 sample=DBModelR::ModelDefinition(
104 table="sample",
105 fields=list(
106 name="TEXT",
107 path="TEXT",
108 polarity="TEXT",
109 kind="TEXT", ## rdata or mxml or enriched_rdata
110 raw="BLOB"
111 ),
112 one=list(
113 "peak_picking_parameters",
114 "pairing_parameters",
115 "alignmenmt_parameters",
116 "camera_parameters",
117 "instrument",
118 "instrument_config",
119 "software",
120 "smol_xcms_set"
121 )
122 ),
123 smol_xcms_set=DBModelR::ModelDefinition(
124 table="smol_xcms_set",
125 fields=list(
126 raw="BLOB"
127 )
128 ),
129 software=DBModelR::ModelDefinition(
130 table="software",
131 fields=list(
132 name="TEXT",
133 version="TEXT"
134 )
135 ),
136 # camera_parameters=DBModelR::ModelDefinition(
137 # table="camera_parameters",
138 # fields=list()
139 # ),
140 # pairing_parameters=DBModelR::ModelDefinition(
141 # table="pairing_parameters",
142 # fields=list()
143 # ),
144 peak_picking_parameters=DBModelR::ModelDefinition(
145 table="peak_picking_parameters",
146 fields=list(
147 ppm="FLOAT",
148 peakwidth="TEXT",
149 snthresh="TEXT",
150 prefilterStep="TEXT",
151 prefilterLevel="TEXT",
152 mzdiff="TEXT",
153 fitgauss="TEXT",
154 noise="TEXT",
155 mzCenterFun="TEXT",
156 integrate="INTEGER",
157 firstBaselineCheck="TEXT",
158 snthreshIsoROIs="TEXT",
159 maxCharge="INTEGER",
160 maxIso="INTEGER",
161 mzIntervalExtension="TEXT"
162 )
163 ),
164 alignmenmt_parameters=DBModelR::ModelDefinition(
165 table="alignmenmt_parameters",
166 fields=list(
167 binSize="TEXT",
168 centerSample="TEXT",
169 response="TEXT",
170 distFun="TEXT",
171 gapInit="TEXT",
172 gapExtend="TEXT",
173 factorDiag="TEXT",
174 factorGap="TEXT",
175 localAlignment="INTEGER",
176 initPenalty="TEXT",
177 bw="TEXT",
178 minFraction="TEXT",
179 minSamples="TEXT",
180 maxFeatures="TEXT"
181 )
182 )
183 )