Abundance Data

A class for working with microbiome or ecological abundance data.

Slots

data

A data.frame of abundance values with species as columns and samples as rows

sampleMetadata

A SampleMetadata object of metadata about the samples with samples as rows and metadata variables as columns

recordIdColumn

The name of the column containing IDs for the samples. All other columns will be treated as abundance values.

ancestorIdColumns

A character vector of column names representing parent entities of the recordIdColumn.

imputeZero

A logical indicating whether NA/ null values should be replaced with zeros.

removeEmptyRecords

A logical indicating whether empty (all NA/ zero) samples should be removed.