filterTaxonMatrix: Filter taxa in an abundance matrix

View source: R/barebonesCoNet.R

filterTaxonMatrixR Documentation

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.