get_count {MicrobiotaProcess} | R Documentation |
Caculate the count or relative abundance of replicate element with a speficify columns
get_count(data, featurelist) get_ratio(data, featurelist)
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. |
mean of data.frame by featurelist
Shuangbin Xu
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])