topf: Make filter fun. that returns the top f fraction of taxa in a...

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

Make filter fun. that returns the top f fraction of taxa in a sample.

Description

As opposed to topp, which gives the most abundant p fraction of observed taxa (richness, instead of cumulative abundance. Said another way, topf ensures a certain fraction of the total sequences are retained, while topp ensures that a certain fraction of taxa/species/OTUs are retained.

Usage

topf(f, na.rm=TRUE)

Arguments

f	Single numeric value between 0 and 1.
na.rm	Logical. Should we remove NA values. Default TRUE.

Value

A function (enclosure), suitable for filterfun_sample, that will return TRUE for each element in the taxa comprising the most abundant f fraction of individuals.

See Also

topk, topf, topp, rm_outlierf

Examples

t1 <- 1:10; names(t1)<-paste("t", 1:10, sep="")
topf(0.6)(t1)
## 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(topf(0.4))
(wh1 <- genefilter_sample(testOTU, f1, A=1))
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.