RbioRXN (version 1.3.1)

is.generic.rhea: Check given reaction is generic reaction

Description

Generic reaction is a reaction with at least one compound class as reaction participant (e.g., a primary alcohol + NADP -> an aldehyde + H(+) + NADPH). This function checks if given reaction is generic reaction

Usage

is.generic.rhea(equation,chebi_df,id_col,parent_col,formula_col,direction_type)

Arguments

equation

Reaction equation usually generated by get.rhea.all() function.

chebi_df

Chemial table data.frame() containing molecular formula and parent compound

id_col

In chemical table, choose the column name which contains chemical id (usually first column)

parent_col

In chemical table, choose the column name which contains parent compound ("parent" in chebi)

formula_col

In chemical table, choose the column name which contains molecular formula

direction_type

In reaction equation, provide reaction direction symbols. Default is c(' <\\?> ', ' <=> ', ' => ')

Value

• Logical TRUE/FALSE

References

Rhea: http://www.ebi.ac.uk/rhea ChEBI: http://www.ebi.ac.uk/chebi

Examples

data(example) # Load example

chebi = example$chebi
rhea_generic = example$rhea_generic$equationWithChebi
rhea_massbal = example$rhea_massbal
rhea = c(rhea_generic, rhea_massbal)

# Check generic reaction
is.generic.rhea(rhea, chebi, id_col='chebi', parent_col='parent', 
  formula_col='formula', direction_type=c('<=> ', '<\\?> ', '=> '))