rm_outlierf: Set to FALSE any outlier species greater than f fractional...

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

Set to FALSE any outlier species greater than f fractional abundance.

Description

This is for removing overly-abundant outlier taxa, not for trimming low-abundance taxa.

Usage

rm_outlierf(f, na.rm=TRUE)

Arguments

f	Single numeric value between 0 and 1. The maximum fractional abundance value that a taxa will be allowed to have in a sample without being marked for trimming.
na.rm	Logical. Should we remove NA values. Default TRUE.

Value

A function (enclosure), suitable for filterfun_sample.

See Also

topk, topf, topp, rm_outlierf

Examples

t1 <- 1:10; names(t1)<-paste("t", 1:10, sep="")
rm_outlierf(0.15)(t1)
## Use simulated abundance matrix
set.seed(711)
testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)
taxa_sums(testOTU)
f1  <- filterfun_sample(rm_outlierf(0.1))
(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.