get_count {MicrobiotaProcess} | R Documentation

## 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.

### 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])

[Package MicrobiotaProcess version 1.2.2 Index]