keep: Keep samples, classes or features

In jasenfinch/metabolyseR: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data

Keep samples, classes or features

Description

Retain samples, classes or features in an AnalysisData object.

Usage

keepClasses(d, cls = "class", classes = c())

## S4 method for signature 'AnalysisData'
keepClasses(d, cls = "class", classes = c())

keepFeatures(d, features = character())

## S4 method for signature 'AnalysisData'
keepFeatures(d, features = character())

keepSamples(d, idx = "fileOrder", samples = c())

## S4 method for signature 'AnalysisData'
keepSamples(d, idx = "fileOrder", samples = c())

Arguments

d	S4 object of class AnalysisData
cls	info column to use for class information
classes	classes to keep
features	features to remove
idx	info column containing sample indexes
samples	sample indexes to keep

Value

An S4 object of class AnalysisData with specified samples, classes or features retained.

Methods

• keepClasses: Keep classes.

• keepFeatures: Keep features.

• keepSamples: Keep samples.

Examples

library(metaboData)
 d <- analysisData(abr1$neg[,200:300],abr1$fact)
 
 ## Keep classes
 d %>% 
  keepClasses(cls = 'day',classes = 'H')
 
 ## Keep features
 d %>% 
  keepFeatures(features = c('N200','N201'))
 
 ## Keep samples
 d %>% 
  keepSamples(idx = 'injorder',samples = c(1,10))

jasenfinch/metabolyseR documentation built on Sept. 18, 2023, 1:25 a.m.