Required columns in an annotation source

Some annotation_sources, such as LCMS tables (lcms_table), require that certain columns are present in the data.frame. These are defined by slots in the source definition. The name of slots containing the required column names for a source can be retrieved using the required_cols function, which will collect and return the names of slots containing required column names for the object and all of its parent objects.

Usage

required_cols(obj, ...)

# S4 method for class 'annotation_source'
required_cols(obj)

Arguments

obj

an annotation_source object

...

additional source specific inputs

Value

a character vector of slot names

Examples

# prepare object
M <- lcms_table(id_column = "id", mz_column = "mz", rt_column = "rt")

#' # get values for required slots
r <- required_cols(M)

# get slot names for required columns
names(r)
#> NULL