threshrank: Thresholded rank transformation.

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

Description

The lowest thresh values in x all get the value 'thresh'.

Usage

threshrank(x, thresh, keep0s=FALSE, ...)

Arguments

x	(Required). Numeric vector to transform.
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 ranked, (optionally) thresholded numeric vector with length equal to x. Default arguments to rank are used, unless provided as additional arguments.

See Also

transform_sample_counts, rank, threshrankfun

Examples

#
(a_vector <- sample(0:10, 100, TRUE))
threshrank(a_vector, 5, keep0s=TRUE)
data(GlobalPatterns)
GP <- GlobalPatterns
## These three approaches result in identical otu_table
(x1 <- transform_sample_counts( otu_table(GP), threshrankfun(500)) )
(x2 <- otu_table(apply(otu_table(GP), 2, threshrankfun(500)), taxa_are_rows(GP)) )
identical(x1, x2)
(x3 <- otu_table(apply(otu_table(GP), 2, threshrank, thresh=500), taxa_are_rows(GP)) )
identical(x1, x3)

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.