filter.Taxa: Filter Taxonomic Abundance Matrix by Total Counts Or Maximum...

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function filter taxa group by counts or relative abundance. If filter by counts, taxa having total counts more than a threshhold will be kept. If filter by relative abundance, taxa with the maximum relative abundance greater than a threshhold in at least one subject will be kept.

Usage

filter.Taxa(taxa, drop.unclassified=TRUE,
            percent=NULL, number=NULL)

Arguments

taxa	the taxonomy abundance matrix: sample x species data frame. See also tax.abund
drop.unclassified	logical, whether or not remove unclassified groups. See also tax.abund
percent	a floating point greater than 0 and less or equals to 1. Filter Taxa table by relative abundance.
number	an integer. FilterTaxa table by total sequence counts.

Value

The value returned by this function is a data frame with taxa met the filter requirement only.

Author(s)

Wen Chen

Examples

data(ITS1)
g1 <- tax.abund(ITS1, rank="g", drop.unclassified=TRUE)
taxa.fil <- filter.Taxa(g1, percent=0.01)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-3
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
[1] "12 taxa met the filter requirment"

RAM documentation built on May 2, 2019, 3:04 p.m.