format_db: Format dataframe of compounds from a database

In shutinet/metabSeek: Search in several databases metabolites masses or spectras

Description

Format each entry of a compound database

1. remove duplicated column according their names

2. replace each space in column names by an underscore

3. remove duplicated or empty primary key (first column)

4. format each text entry @seealso format_text

5. format charge entries @seealso format_int

6. format chemical formulas @seealso format_formula

7. format InChIKeys @seealso format_inchikey

8. compute basepeak masses with enviPat

Usage

format_db(data)

Arguments

data	matrix, must contains columns: id name synonyms smiles inchikey formula charge ...

Value

dataframe with formatted columns

• id

• name

• synonym

• smiles

• inchikey

• formula

• charge

• ...

• basepeak_mass

shutinet/metabSeek documentation built on Sept. 5, 2020, 12:57 a.m.