Hi, 

Im working with a 53 sample of OTU sequences and I was hoping to create a new MRexperiment with a subset of the samples. I would like to use the sample name as the feature for which to select the samples by.

I am able to use the:  samplesToKeep = which(pData(obj)$sampleName == "XX") command and with the "featuresToKeep" i can create a new MR experiment. but I can only achieve to get one sample at a time using the sample name, so I go from :

MRexperiment (storageMode: environment)
assayData: 1319558 features, 53 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: Yf 717 ... P4 (53 total)
  varLabels: ProjectName LinkerPrimerSequence ... BarcodeName (5 total)
  varMetadata: labelDescription
featureData
  featureNames: denovo0 denovo1 ... denovo1319557 (1319558 total)
  fvarLabels: taxonomy1 taxonomy2 ... taxonomy8 (8 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'

to

MRexperiment (storageMode: environment)
assayData: 1319558 features, 1 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: Yc
  varLabels: ProjectName LinkerPrimerSequence ... BarcodeName (5 total)
  varMetadata: labelDescription
featureData
  featureNames: denovo0 denovo1 ... denovo1319557 (1319558 total)
  fvarLabels: taxonomy1 taxonomy2 ... taxonomy8 (8 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'

Is there a way that I can get add more than one samples to the subset? or if I separate the samples individually, is there a way I can merge those MRexperiment??

thank you for your time

msd16s is just an example dataset. Another example is mouseData. I highlight below. But for your specific it looks like you'll have to specify the samples you're interested in, either by index or sample name.

samplesToKeep = c("Yf","717","718")

obj2 = obj[,samplesToKeep]

To add metadata you can use the pData(obj)$variableName = vector or fData(obj)$variableName, but be careful with consistency and ordering of sample values.

> data(mouseData)

> mouseData
MRexperiment (storageMode: environment)
assayData: 10172 features, 139 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: PM1:20080107 PM1:20080108 ... PM9:20080303 (139 total)
  varLabels: mouseID date ... status (5 total)
  varMetadata: labelDescription
featureData
  featureNames: Prevotellaceae:1 Lachnospiraceae:1 ...
    Parabacteroides:956 (10172 total)
  fvarLabels: superkingdom phylum ... OTU (7 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
> mouseData[,pData(mouseData)$mouseID=="PM1"]
MRexperiment (storageMode: environment)
assayData: 10172 features, 12 samples 
  element names: counts 
protocolData: none
phenoData
  sampleNames: PM1:20080107 PM1:20080108 ... PM1:20080303 (12 total)
  varLabels: mouseID date ... status (5 total)
  varMetadata: labelDescription
featureData
  featureNames: Prevotellaceae:1 Lachnospiraceae:1 ...
    Parabacteroides:956 (10172 total)
  fvarLabels: superkingdom phylum ... OTU (7 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  

Hi rleonzay,

If each sample has an independent sample name then `which(pData(obj)$sampleName=="XX")` is going to return the column index for sample "XX". However, you can create a general vector for the samples of interest to subset the obj.

As an example the data vignette for msd16s [http://bioconductor.org/packages/release/data/experiment/vignettes/msd16s/inst/doc/msd16s.pdf] shows a few subsetting examples. If you're still unable to subset the MRexperiment object, feel free to send me an MRE and I'll show you specifically how.

Best,