Question: How to remove samples from EDAseq SeqExpressionSeq
0
gravatar for Jon Bråte
8 months ago by
Jon Bråte160
Norway
Jon Bråte160 wrote:

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 • 188 views
ADD COMMENTlink modified 8 months ago by davide risso830 • written 8 months ago by Jon Bråte160
Answer: How to remove samples from EDAseq SeqExpressionSeq
1
gravatar for davide risso
8 months ago by
davide risso830
Weill Cornell Medicine
davide risso830 wrote:

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:
ADD COMMENTlink modified 8 months ago • written 8 months ago by davide risso830

Thanks! That's perfect.

Jon

ADD REPLYlink written 8 months ago by Jon Bråte160
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