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

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

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)

Example output

OTU Table:          [2 taxa and 5 samples]
                     taxa are columns
    sp3 sp4
sa1  13  48
sa2  31  36
sa3  44  36
sa4  42  47
sa5  48  40
OTU Table:          [3 taxa and 5 samples]
                     taxa are columns
    sp1 sp2 sp3
sa1  15   7  13
sa2  22  16  31
sa3  17   4  44
sa4  32  29  42
sa5  23  33  48

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