Data manipulation

Import example data

  • Load demo data (OMA section 3.3).

  • Extra: create the data straight from source files in the shared data folder (OMA section 3.4).

Investigate the data elements

Extract the microbiota data elements (ch 3.2):

  • column data (sample data)
  • row data (feature data)
  • assays (abundance matrices)
  • other data elements

Subsetting

  • Show how to subset microbiota data (ex. 17.3.1)

  • Subset to the most prevalent taxa (17.3.3) (tip: subsetByPrevalentFeatures)

    • for count assay; how many features remain?
    • for relative abundance assay; how many features remain?

Agglomeration

Agglomerate the microbiota data to higher taxonomic levels:

  • chapter 6.3
  • agglomerateByRank

Extra exercises 17.3

  • library sizes & rarification (17.3.2)

Exercises 17.5.1-17.5.2: colData & diversity

  • Add Shannon diversity in colData
  • Visualize diversity differences between sample groups

Transformations

  • transform to alternative assays and show histograms for the whole assay
  • transform to alternative assays; boxplots for selected feature