How to exclude columns of phenoData of ExpressionSet Data in R

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8.6 years ago

floodking • 0

I want to select columns from phenoData of ExpressionSet in R. My data to be processes is teset.

class(teset)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"

teset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 19420 features, 253 samples 
 element names: exprs
   protocolData: none
phenoData
  sampleNames: TCGA-CV-7091-01A-11D-2012-08 TCGA-CJ-4875-01A-01D-1373-10 ...
    TCGA-25-1626-01A-01W-0615-10 (253 total)
  varLabels: time status ... Tumor_grade (7 total)
  varMetadata: labelDescription
featureData
  featureNames: 1060P11.3 A1BG ... ZZZ3 (19420 total)
  fvarLabels: EntrezID Symbol Desc Synonyms
  fvarMetadata: labelDescription
 experimentData: use 'experimentData(object)'
Annotation:

covariates information of teset:

names(pData(teset))
[1] "time"            "status"          "Age"             "Gender"         
[5] "TCGA_tumor_type" "Tumor_stage"     "Tumor_grade"

I only want a teset data without the first two columns in pData, namely all exprs data with pData(teset)[,-c(1,2)]. How can I do this? Thanks for help!!!

biconductor R ExpressionSet • 3.1k views

ADD COMMENT • link 8.6 years ago by floodking • 0

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You don't need to change or exclude anything, just don't include those terms in your model.