MetaboSet-class: An S4 class used to represent LC-MS datasets

In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

An S4 class used to represent LC-MS datasets

Description

MetaboSet is the main class used to represent data in the notame package. It is built upon the ExpressionSet class from the Biobase package. For more information, read the MetaboSet utility vignette. In addition to the slots inherited from ExpressionSet, MetaboSet has three slots of its own. The extra three slots hold special column names that are stored purely for convenience, as many functions use these as defaults.

Usage

## S4 method for signature 'MetaboSet'
combined_data(object)

## S4 method for signature 'MetaboSet'
combined_data(object)

## S4 method for signature 'MetaboSet'
group_col(object)

## S4 method for signature 'MetaboSet'
time_col(object)

## S4 method for signature 'MetaboSet'
subject_col(object)

## S4 method for signature 'MetaboSet'
flag(object)

## S4 method for signature 'MetaboSet,data.frame'
join_fData(object, dframe)

## S4 method for signature 'MetaboSet,data.frame'
join_pData(object, dframe)

Arguments

object

a MetaboSet object

Methods (by generic)

• combined_data(MetaboSet): sample information and features combined to a single data frame, one row per sample

• combined_data(MetaboSet): sample information and features combined to a single data frame, one row per sample

• group_col(MetaboSet): access and set group_col

• time_col(MetaboSet): access and set time_col

• subject_col(MetaboSet): access and set subject_col

• flag(MetaboSet): access and set results

• join_fData(object = MetaboSet, dframe = data.frame): join new information to fData

• join_pData(object = MetaboSet, dframe = data.frame): join new information to fData

Slots

group_col

character, name of the column holding group information

time_col

character, name of the column holding time points

subject_col

character, name of the column holding subject identifiers

antonvsdata/notame documentation built on Sept. 14, 2024, 11:09 p.m.