RAM (version 1.2.0)

filter.OTU: Filter OTU

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

Examples

data(ITS1, ITS2, meta)
data<-list(ITS1=ITS1, ITS2=ITS2)
otu.001 <- filter.OTU(data=data, percent=0.01)
length(otu.001)
names(otu.001)
otu.50 <- filter.OTU(data=data, number=50)