Remove samples, classes or features — removeClasses • metabolyseR

Exclusion of samples, classes or features from an AnalysisData object.

Usage

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

# S4 method for AnalysisData
removeClasses(d, cls = "class", classes = c())

removeFeatures(d, features = character())

# S4 method for AnalysisData
removeFeatures(d, features = character())

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

# S4 method for AnalysisData
removeSamples(d, idx = "fileOrder", samples = c())

Arguments

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

Value

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

Methods

removeClasses: Remove classes.
removeFeatures: Remove features.
removeSamples: Remove samples.

Examples

library(metaboData)
 d <- analysisData(abr1$neg[,200:300],abr1$fact)
 
 ## Remove classes
 d %>% 
  removeClasses(cls = 'day',classes = 'H')
#> 
#> AnalysisData object containing:
#> 
#> Samples: 100 
#> Features: 101 
#> Info: 9 
#> 
 
 ## Remove features
 d %>% 
  removeFeatures(features = c('N200','N201'))
#> 
#> AnalysisData object containing:
#> 
#> Samples: 120 
#> Features: 99 
#> Info: 9 
#> 
 
 ## Remove samples
 d %>% 
  removeSamples(idx = 'injorder',samples = c(1,10))
#> 
#> AnalysisData object containing:
#> 
#> Samples: 118 
#> Features: 101 
#> Info: 9 
#>