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

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

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.

Value

mean of data.frame by featurelist

Author(s)

Shuangbin Xu

Examples

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])

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.