Reads SLIMM output to a data table.

Reads SLIMM output to a data table.

read_slimm(reports)

Arguments

reports

Where the slimm output is stored.

Value

A data table counting reads and relative abundances for all found bacteria for several taxonomic ranks. It will contain the following columns:

  • idid of the sample

  • rankthe name of the taxonomic rank, for instance "genus"

  • namethe value of the rank, for instance "Escherichia"

  • readsthe number of reads in that rank

  • relativethe relative abundance of the rank in [0,1]

  • coveragethe coverage of the rank

Examples

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#> NULL