adap.to.rc | R Documentation |
use pubchem rest and view APIs to retreive structures, CIDs (if a name or inchikey is given), synonyms, and optionally vendor data, when available.
adap.to.rc( seq = NULL, spec.abund = NULL, msp = NULL, annotations = NULL, mzdec = 0, min.score = 700, manual.name = TRUE, qc.tag = "qc", blank.tag = "blank" )
seq |
file name/path to sequence file - expect filenames in column 1 and sample names in column 2. filenames should match those in spec.abund |
spec.abund |
file name/path to adap-big export of signal intensities. .csv file expected |
msp |
file name/path to .msp file created by adap-big |
annotations |
file name/path to annotations .xlsx file. generally 'simple_export.xlsx' |
mzdec |
mz decimals to report for internal storage/reporting. generally we want 0 for adap kdb |
min.score |
700 (out of 1000) by default |
manual.name |
when looking up inchikey/names, should manual input be used to fill ambiguous names? generally recommend TRUE |
qc.tag |
a character string by which to recognize a sample as a qc sample. i.e. 'QC' or 'qc'. |
blank.tag |
a character string by which to recognize a sample as a blank sample. i.e. 'blank' or 'Blank'. |
useful for moving from chemical name to digital structure represtation. greek letters are assumed to be 'UTF-8' encoded, and are converted to latin text before searching. if you are reading in your compound name list, do so with 'encoding' set to 'UTF-8'.
returns a ramclustR structured object suitable for down stream processing steps.
Corey Broeckling
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