get_alphaindex: alpha index

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

alpha index

Description

calculate the alpha index (Obseve,Chao1,Shannon,Simpson) of sample with diversity

Usage

get_alphaindex(obj, ...)

## S4 method for signature 'matrix'
get_alphaindex(obj, mindepth, sampleda, force = FALSE, ...)

## S4 method for signature 'data.frame'
get_alphaindex(obj, ...)

## S4 method for signature 'integer'
get_alphaindex(obj, ...)

## S4 method for signature 'numeric'
get_alphaindex(obj, ...)

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

Arguments

obj	object, data.frame of (nrow sample * ncol taxonomy(feature)) or phyloseq.
...	additional arguments.
mindepth	numeric, Subsample size for rarefying community.
sampleda	data.frame,sample information, row sample * column factors.
force	logical whether calculate the alpha index even the count of otu is not rarefied, default is FALSE. If it is TRUE, meaning the rarefaction is not be performed automatically.

Value

data.frame contained alpha Index.

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)] %>% t() %>% 
          data.frame(check.names=FALSE)
set.seed(1024)
alphatab <- get_alphaindex(otuda)
head(as.data.frame(alphatab))
data(test_otu_data)
class(test_otu_data)
test_otu_data %<>% as.phyloseq()
class(test_otu_data)
set.seed(1024)
alphatab2 <- get_alphaindex(test_otu_data)
head(as.data.frame(alphatab2))

## End(Not run)

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.