raw_data class

raw_data class

Usage

raw_data(metabolomics_matrix, LOD_table, metabolites, group = NULL)

Arguments

metabolomics_matrix

a data.frame, matrix containing biocrates data

LOD_table

a list containing two elements:

• table: LOD table of limits of detection / quantification,

• types: character vector of types of values, for example calc. meaning calculated from samples and op, received from operator.

metabolites

a character, vector of metabolites names contained in the data.

group

a NULL indicating no grouping or a vector of character names of group columns. Default to NULL. The code will throw an error in the case when:

• column of such a name won't be contained in the dataset,

• there will be NA's in the grouping column,

• any group will have less than 2 observations.

Value

raw_data object metabolomics matrix with the following attributes:

• LOD_table

• NA_info: a list related to missing values in the data. It contains NA_ratios: fractions of missing values per every metabolite. When group parameter (see below) is provided and counts: table of types of missing values with their counts (related to "sample" type samples).

• metabolites

• samples: a data.frame containing names of samples types and their counts

• group : a character name of group from the table

• removed: a list of removed metabolites

• plate bar code: each measurement has two plate bar codes depending on the method used