How to remove samples from EDAseq SeqExpressionSeq
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Jon Bråte ▴ 180
@jon-brate-6263
Last seen 13 days ago
Norway

I have created a new SeqExpressionSet and I would like to remove different samples to see the effects on downstream analyses. Can I remove the samples, including the metadata information, directly from the SeqExpressionSet?

Here is my object:

> set
SeqExpressionSet (storageMode: lockedEnvironment)
assayData: 54232 features, 48 samples 
  element names: counts, normalizedCounts, offset 
protocolData: none
phenoData
  sampleNames: Sample_01-21-1 Sample_02-21-4 ... Sample_48-17-4
    (48 total)
  varLabels: Sample Stage ... ERCC_ratio (9 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:
EDAseq • 520 views
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Entering edit mode
davide risso ▴ 870
@davide-risso-5075
Last seen 5 months ago
University of Padova

Hi Jon,

yes, simply subsetting the SeqExpressionSet will subset both expression data and metadata (if by metadata you mean what in ExpressionSet jargon are called phenoData and featureData, i.e., sample and gene metadata).

Example:

> library(EDASeq)
> example("betweenLaneNormalization")
> data
SeqExpressionSet (storageMode: lockedEnvironment)
assayData: 6685 features, 4 samples 
  element names: counts, normalizedCounts, offset 
protocolData: none
phenoData
  sampleNames: mut_1 mut_2 wt_1 wt_2
  varLabels: conditions
  varMetadata: labelDescription
featureData
  featureNames: YHR055C YPR161C ... YAR061W (6685 total)
  fvarLabels: gc
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> data[1:10,1:3]
SeqExpressionSet (storageMode: lockedEnvironment)
assayData: 10 features, 3 samples 
  element names: counts, normalizedCounts, offset 
protocolData: none
phenoData
  sampleNames: mut_1 mut_2 wt_1
  varLabels: conditions
  varMetadata: labelDescription
featureData
  featureNames: YHR055C YPR161C ... YAL069W (10 total)
  fvarLabels: gc
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
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Entering edit mode

Thanks! That's perfect.

Jon

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