prevalence_crop: Subset dataset by minimum OTU prevalence
In dlemas/microbes: tools for analyzing microbiome data

Description Usage Arguments Details Value Author(s) Examples

Subset df.counts or df.ra by a selected minimum prevalence level.

1	prevalence_crop(df, x)

`df`	df.counts or df.normed
`x`	Desired minimum prevalence level

This function works best with df.ra

The output is a subset of the original data frame with the same formatting.

atomczik

## The function is currently defined as
function (df, x) 
{
    n <- length(row.names(df))
    m <- length(df)
    k <- m + 1
    for (i in 1:n) {
        df$blank[i] <- (sum((df[i, ]) <= 1e-07))
    }
    df <- subset(df, !(df$blank >= ((1 - x) * m)))
    df <- df[, -k]
    return(df)
  }