threshrankfun: A closure version of the 'threshrank' function.

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

A closure version of the threshrank function.

Description

Takes the same arguments as threshrank, except for x, because the output is a single-argument function rather than a rank-transformed numeric. This is useful for higher-order functions that require a single-argument function as input, like transform_sample_counts.

Usage

threshrankfun(thresh, keep0s=FALSE, ...)

Arguments

thresh	A single numeric value giving the threshold.
keep0s	A logical determining whether 0's in x should remain a zero-value in the output. If FALSE, zeros are treated as any other value.
...	Further arguments passes to the rank function.

Value

A single-argument function with the options to threshrank set.

See Also

transform_sample_counts, threshrankfun, threshrank

Examples

data(esophagus)
x1 = transform_sample_counts(esophagus, threshrankfun(50))
otu_table(x1)
x2 = transform_sample_counts(esophagus, rank)
otu_table(x2)
identical(x1, x2)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.