filter.OTU: Filter OTU

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

Description

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

Usage

filter.OTU(data, percent=NULL, number=NULL)

Arguments

data	a list of otu tables to be processed. See also RAM.input.formatting
percent	a floating point greater than 0 and less or equals to 1. Filter OTU table by relative abundance.
number	an integer. Filter OTU table by counts.

Value

The value returned by this function is a list of filtered otu tables provided by the user

Author(s)

Wen Chen

Examples

data(ITS1, ITS2, meta)
data<-list(ITS1=ITS1, ITS2=ITS2)
## Not run: 
otu.001 <- filter.OTU(data=data, percent=0.01)
length(otu.001)
names(otu.001)
otu.50 <- filter.OTU(data=data, number=50)

## End(Not run)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: ggplot2
[1] "26 otus in ITS1 met the filter requirment."
[1] "30 otus in ITS2 met the filter requirment."
[1] 2
[1] "ITS1" "ITS2"
[1] "118 otus in ITS1 met the filter requirment."
[1] "129 otus in ITS2 met the filter requirment."

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