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How to delete the cells belongs to particlar CellType in R?
1
Entering edit mode
19 months ago
Jon • 90
United States

Hi, Below is what I have,

    >DCX
    CellDataSet (storageMode: environment)
    assayData: 22995 features, 64 samples 
      element names: exprs 
    protocolData: none
    phenoData
      sampleNames: CN01 CN02 ... CN64 (64 total)
      varLabels: V1 Size_Factor ... CellType (10 total)
      varMetadata: labelDescription
    featureData
      featureNames: 0610007P14Rik 0610009B22Rik ... Zzz3 (22995 total)
      fvarLabels: gene_short_name num_cells_expressed use_for_ordering
      fvarMetadata: labelDescription
    experimentData: use 'experimentData(object)'
    Annotation:

> head(pData(DCX))
       V1 Size_Factor num_genes_expressed Cluster peaks  halo     delta
CN01 CN01    1.907703                5062       3 FALSE FALSE 0.5659337
CN02 CN02    2.659821                7054       2 FALSE FALSE 0.5043280
CN03 CN03    2.389068                7099       4 FALSE FALSE 0.3798056
CN04 CN04    1.832047                7099       2 FALSE FALSE 0.6221111
CN05 CN05    1.784817                6444       2 FALSE FALSE 0.5936016
CN06 CN06    2.762373                5910       3 FALSE FALSE 0.5549383
           rho nearest_higher_density_neighbor        CellType
CN01 0.7087620                              NA OLIGODENDROCYTE
CN02 1.1789535                              NA          NEURON
CN03 0.7203490                              NA       ASTROCYTE
CN04 1.3089645                              NA          NEURON
CN05 0.3867494                              NA          NEURON
CN06 0.3565931                              NA OLIGODENDROCYTE

How can I delete the all cells which belongs to NEURON celltype?

Please help, I am new to R!

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1
Entering edit mode
19 months ago
National Institutes of Health, Bethesda…
DCX2 = DCX[, pData(DCX)$CellType != "NEURON"]
table(pData(DCX2)$CellType)
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thanks, but not working!

> DCX2 = DCX[pData(DCX)$CellType != "NEURON", ]
> table(pData(DCX2)$CellType)

      ASTROCYTE          NEURON OLIGODENDROCYTE      RADIALGLIA 
             15              17              21              11

p.s. I want to delete all the corresponding samples/cell numbers in "DCX object" which is classified as 'NEURON'.

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Sorry. Typo in my original reply--should be fixed now. Just a note that understanding how these objects work is pretty important, so you might have noticed that my answer was incorrectly subsetting the "genes" rather than the "samples".

In any case, I have fixed my answer.

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thank you so much! now i understood!

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