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

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

MetaboSet is the main class used to represent data in the amp 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 four slots of its own. The first three slots hold special column names that are stored purely for convenience, as many functions use these as defaults. The fourth slot is a data frame with one row per feature that holds all relevant results from the analyses.

Usage

## 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'
results(object)

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

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

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

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

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

## S4 method for signature 'MetaboSet'
flag_quality(object,
  condition = "(RSD_r < 0.2 & D_ratio_r < 0.4) |\n                                (RSD < 0.1 & RSD_r < 0.1 & D_ratio < 0.1)")

## S4 method for signature 'MetaboSet'
flag_detection(object, qc_limit = 0.7,
  group_limit = 0.8, group = group_col(object))

Methods (by generic)

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

• group_col: access and set group_col

• time_col: access and set time_col

• subject_col: access and set subject_col

• results: access and set results

• flag: access and set results

• join_results: join new information to results

• join_fData: join new information to fData

• quality: extract quality information of features

• assess_quality: compute quality metrics

• flag_quality: flag low-quality features

• flag_detection: flag features with low detection rate

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

results

data frame, holds results of analyses

antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.