Filter taxa in an abundance matrix

Discard taxa with less than the given minimum number of occurrences.

filterTaxonMatrix(
  x,
  minocc = 0,
  keepSum = FALSE,
  return.filtered.indices = FALSE
)

Arguments

x	taxon abundance matrix, rows are taxa, columns are samples
minocc	minimum occurrence (minimum number of samples with non-zero taxon abundance)
keepSum	If keepSum is true, the discarded rows are summed and the sum is added as a row with name: summed-nonfeat-rows
return.filtered.indices	if true, return an object with the filtered abundance matrix in mat and the indices of removed taxa in the original matrix in filtered.indices

Value

filtered abundance matrix