jjjermiah / annotationgx

jermiah

Software Developer and Bioinformatics Analyst at the BHKLab, Princess Margaret Cancer Research Centre

Welcome to my page! I am a Western University Alumni with a MSc. in Medical Biophysics and a BSc. in Integrated Science specializing in Computer Science.

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This area is a work in progress. I will be adding more languages and tools as I learn them.

annotationgx's Issues

Return failed queries as an attribute to getPubchemCompound

currently only returns successful founds cids, extra steps to re-search with another query is redundant

PUGREST.NotFound being returned when cant find

(compound_nameToCIDS <- AnnotationGx::getPubchemCompound(
    ann_cols[1:20, broad_cpd_id],
    from='name',
    to='cids',
))

name             cids
           <char>           <char>
 1: BRD-K46556387 PUGREST.NotFound
 2: BRD-K86574132 PUGREST.NotFound
 3: BRD-K35716340 PUGREST.NotFound
 4: BRD-K89692698 PUGREST.NotFound
 5: BRD-A18763547 PUGREST.NotFound
 6: BRD-K89329876 PUGREST.NotFound
 7: BRD-K64634304 PUGREST.NotFound
 8: BRD-K45401373 PUGREST.NotFound
 9: BRD-K15563106 PUGREST.NotFound
10: BRD-A93255169 PUGREST.NotFound
11: BRD-K19295594 PUGREST.NotFound
12: BRD-K29458283 PUGREST.NotFound
13: BRD-K24844714 PUGREST.NotFound
14: BRD-K33583600 PUGREST.NotFound
15: BRD-K34157611 PUGREST.NotFound
16: BRD-K03406345 PUGREST.NotFound
17: BRD-K89732114 PUGREST.NotFound
18: BRD-A28746609 PUGREST.NotFound
19: BRD-K93754473 PUGREST.NotFound
20: BRD-K11626735 PUGREST.NotFound
             name             cids