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ProbMetab For Galaxy
http://workflow4metabolomics.org/
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create.reactionM #2

Open lecorguille opened 8 years ago

lecorguille commented 8 years ago

Using a test-data generate from faahKO_reduce.zip:

> reactionM = create.reactionM(DB, ionAnnot, ppm.tol=listArguments[["ppm_tol"]])
There were 50 or more warnings (use warnings() to see the first 50)
> warnings()
Warning messages:
1: In f.extract(formula) : Invalid formula:C2H4NO2R(C2H2NOR)n
2: In f.extract(formula) : Invalid formula:C2H4NO2R(C2H2NOR)n
3: In f.extract(formula) : Invalid formula:C10H17O8PR2(C5H8O5PR)n
4: In f.extract(formula) : Invalid formula:C10H17O8PR2(C5H8O5PR)n
5: In formula2mass(as.character(x)) : Invalid formula:C22H35N7O17P3SR
6: In formula2mass(as.character(x)) : Invalid formula:C2H4NO2R
7: In f.extract(formula) : Invalid formula:C10H18O13P2R2(C5H8O6PR)n
8: In f.extract(formula) : Invalid formula:C10H18O13P2R2(C5H8O6PR)n
9: In formula2mass(as.character(x)) : Invalid formula:CO2R
10: In f.extract(formula) : Invalid formula:C10H17O10PR2(C5H8O6PR)n
11: In f.extract(formula) : Invalid formula:C10H17O10PR2(C5H8O6PR)n
12: In formula2mass(as.character(x)) : Invalid formula:HOR
13: In formula2mass(as.character(x)) : Invalid formula:CHOR
14: In f.extract(formula) : Invalid formula:C2H4NO2R(C2H2NOR)n
15: In formula2mass(as.character(x)) : Invalid formula:C4H6N2O3R2
16: In f.extract(formula) : Invalid formula:C20H37O4P(C5H8)n
17: In f.extract(formula) : Invalid formula:C20H37O4P(C5H8)n
18: In formula2mass(as.character(x)) : Invalid formula:C42H44FeN8O8S2R4
19: In formula2mass(as.character(x)) : Invalid formula:C42H44FeN8O8S2R4
20: In formula2mass(as.character(x)) : Invalid formula:HSR
21: In formula2mass(as.character(x)) : Invalid formula:C2H4NO2R
22: In formula2mass(as.character(x)) : Invalid formula:C10H18NO8PR2
23: In formula2mass(as.character(x)) : Invalid formula:C2HO3R
24: In formula2mass(as.character(x)) : Invalid formula:CHO2R
25: In formula2mass(as.character(x)) : Invalid formula:C5H6O5R2
26: In formula2mass(as.character(x)) : Invalid formula:C5H10O7PR
27: In f.extract(formula) : Invalid formula:C10H19O16P3R2(C5H8O6PR)n
28: In f.extract(formula) : Invalid formula:C10H19O16P3R2(C5H8O6PR)n
29: In formula2mass(as.character(x)) : Invalid formula:C3H4OSR2
30: In formula2mass(as.character(x)) : Invalid formula:C12H9N4O2R
31: In formula2mass(as.character(x)) : Invalid formula:C19H36NO3R
32: In f.extract(formula) : Invalid formula:C13H11N2. CH3SO4
33: In f.extract(formula) : Invalid formula:C13H11N2. CH3SO4
34: In formula2mass(as.character(x)) : Invalid formula:C5H12O13P3R
35: In f.extract(formula) : Invalid formula:C53H79CoN11O14P(R1)(R2)
36: In f.extract(formula) : Invalid formula:C4H6N2O3R2(C7H9N2O2R)n
37: In f.extract(formula) : Invalid formula:C4H6N2O3R2(C7H9N2O2R)n
38: In f.extract(formula) : Invalid formula:C16H18N3S. Cl
39: In f.extract(formula) : Invalid formula:C12H14N2. 2Cl
40: In formula2mass(as.character(x)) : Invalid formula:CH3OR
41: In formula2mass(as.character(x)) : Invalid formula:HSR
42: In formula2mass(as.character(x)) : Invalid formula:C15H25O16P2R3
43: In formula2mass(as.character(x)) : Invalid formula:CH2NOR
44: In formula2mass(as.character(x)) : Invalid formula:C24H37N7O18P3SR
45: In formula2mass(as.character(x)) : Invalid formula:C14H19N3O15P2R2
46: In formula2mass(as.character(x)) : Invalid formula:SR2
47: In f.extract(formula) : Invalid formula:C18H33N3O10(R1)(R2)
48: In formula2mass(as.character(x)) : Invalid formula:CH3OR
49: In formula2mass(as.character(x)) : Invalid formula:C10H14N4O4S2R4
50: In formula2mass(as.character(x)) : Invalid formula:C10H12N4O4S2R4