filterTaxonMatrix: Filter taxa in an abundance matrix

In hallucigenia-sparsa/seqgroup: Analysis of Sequencing Data with Groups

Filter taxa in an abundance matrix

Description

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

Usage

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

hallucigenia-sparsa/seqgroup documentation built on July 6, 2022, 1:11 p.m.