Question: How to remove samples from EDAseq SeqExpressionSeq
0
gravatar for Jon Bråte
11 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 • 230 views
ADD COMMENTlink modified 11 months ago by davide risso830 • written 11 months ago by Jon Bråte160
Answer: How to remove samples from EDAseq SeqExpressionSeq
1
gravatar for davide risso
11 months ago by
davide risso830
University of Padova
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 11 months ago • written 11 months ago by davide risso830

Thanks! That's perfect.

Jon

ADD REPLYlink written 10 months ago by Jon Bråte160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 406 users visited in the last hour