filterfun_sample: A sample-wise filter function builder analogous to...

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

A sample-wise filter function builder analogous to filterfun.

Description

See the filterfun, from the Bioconductor repository, for a taxa-/gene-wise filter (and further examples).

Usage

filterfun_sample(...)

Arguments

...	A comma-separated list of functions.

Value

An enclosure (function) that itself will return a logical vector, according to the functions provided in the argument list, evaluated in order. The output of filterfun_sample is appropriate for the ‘flist’ argument to the genefilter_sample method.

See Also

filterfun, genefilter_sample

Examples

# Use simulated abundance matrix
set.seed(711)
testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)
f1  <- filterfun_sample(topk(2))
wh1 <- genefilter_sample(testOTU, f1, A=2)
wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE)
prune_taxa(wh1, testOTU)
prune_taxa(wh2, testOTU)

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