label#
The purpose of this command is to take a .csv (or .feather) of compound time series data and output an integrated time series of functional groups.
From the format discussed on the integrate-peaks guide, to a table that looks like this:
func group 1 |
func group 2 |
… |
|
|---|---|---|---|
timestamp 1 |
# |
# |
# |
timestamp 2 |
# |
# |
# |
… |
# |
# |
# |
The label command takes the same optional arguments as
integrate-peaks to describe your input and customize your output. Pass -ts, --tscol
with the name of your timestamp column if there is one in your input file. Pass -i, --ignore with the
names of any metadata columns that you want to be passed from input to output. Choose whether you want to
sum functional groups by molecular formula (-col=mf) or SMILES (-col=smiles). If molecular formula
is chosen, then functional groups corresponding to all of the isomers within our
database will be used. If SMILES is chosen, then only the specific
functional groups for the single isomer denoted by the SMILES string are used. As always, specify your
output path with -o, --output.
Note on Molecular Identifiers
To read more about molecular formula vs SMILES in this context, see more.
Below is an example command where integrated_data.csv, is labeled / integrated by functional group and saved to labeled_data.csv.
integrated_data.csv has a timestamp column named ‘Time’, and columns denoted by molecular formula.
$ tofspec label -o labeled_data.csv -ts Time -col=mf integrated_data.csv