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 = "seq.csv",
spec.abund = "signal.csv",
msp = "spectra.msp",
annotations = "annotations.xlsx",
mzdec = 1,
min.score = 700,
manual.name = FALSE,
qc.tag = "qc",
blank.tag = "blank",
factor.names = c()
)returns a ramclustR structured object suitable for down stream processing steps.
file name/path to sequence file - expect filenames in column 1 and sample names in column 2. filenames should match those in spec.abund
file name/path to adap-big export of signal intensities. .csv file expected
file name/path to .msp file created by adap-big
file name/path to annotations .xlsx file. generally 'simple_export.xlsx'
mz decimals to report for internal storage/reporting. generally we want 0 for adap kdb
700 (out of 1000) by default
when looking up inchikey/names, should manual input be used to fill ambiguous names? generally recommend TRUE
a character string by which to recognize a sample as a qc sample. i.e. 'QC' or 'qc'.
a character string by which to recognize a sample as a blank sample. i.e. 'blank' or 'Blank'.
factor names
Corey Broeckling
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'.