drop_taxa: Dropping Species with Few abundance and Few Occurrences

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Dropping Species with Few abundance and Few Occurrences

Description

Drop species or features from the feature data frame or phyloseq that occur fewer than or equal to a threshold number of occurrences and fewer abundance than to a threshold abundance.

Usage

drop_taxa(obj, ...)

## S4 method for signature 'data.frame'
drop_taxa(obj, minocc = 0, minabu = 0, ...)

## S4 method for signature 'phyloseq'
drop_taxa(obj, ...)

Arguments

obj	object, phyloseq or a dataframe of species (n_sample, n_feature).
...	additional parameters.
minocc	numeric, the threshold number of occurrences to be dropped, if < 1.0,it will be the threshold ratios of occurrences, default is 0.
minabu	numeric, the threshold abundance, if fewer than the threshold will be dropped, default is 0.

Value

dataframe of new features.

Author(s)

Shuangbin Xu

Examples

## Not run: 
otudafile <- system.file("extdata", "otu_tax_table.txt",
                         package="MicrobiotaProcess")
otuda <- read.table(otudafile, sep="\t", 
                    header=TRUE, row.names=1, 
                    check.names=FALSE, skip=1, 
                    comment.char="")
otuda <- otuda[sapply(otuda, is.numeric)]
otuda <- data.frame(t(otuda), check.names=FALSE)
dim(otuda)
otudat <- drop_taxa(otuda, minocc=0.1, minabu=1)
dim(otudat)
data(test_otu_data)
test_otu_data %<>% as.phyloseq()
keepps <- drop_taxa(test_otu_data, minocc=0.1, minabu=0)

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on July 26, 2024, 4:21 a.m.