get_count: calculate the count or relative abundance of replicate...

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

calculate the count or relative abundance of replicate element with a speficify column

Description

Caculate the count or relative abundance of replicate element with a speficify columns

Usage

get_count(data, featurelist, ...)

get_ratio(data, featurelist, ...)

Arguments

data	dataframe; a dataframe contained one character column and others is numeric, if featurelist is NULL. Or a numeirc dataframe, if featurelist is non't NULL, all columns should be numeric.
featurelist	dataframe; a dataframe contained one chatacter column, default is NULL.
...	additional parameters.

Value

mean of data.frame by featurelist

Author(s)

Shuangbin Xu

Examples

## Not run: 
otudafile <- system.file("extdata", "otu_tax_table.txt", 
                      package="MicrobiotaProcess")
samplefile <- system.file("extdata", 
                 "sample_info.txt", package="MicrobiotaProcess")
otuda <- read.table(otudafile, sep="\t", header=TRUE, 
                    row.names=1, check.names=FALSE, 
                    skip=1, comment.char="")
sampleda <- read.table(samplefile, 
            sep="\t", header=TRUE, row.names=1)
taxdf <- otuda[!sapply(otuda, is.numeric)]
taxdf <- split_str_to_list(taxdf)
otuda <- otuda[sapply(otuda, is.numeric)]
phycount <- get_count(otuda, taxdf[,2,drop=FALSE])
phyratios <- get_ratio(otuda, taxdf[,2,drop=FALSE])

## End(Not run)

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