topp: Make filter fun. that returns the most abundant 'p' fraction...

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

Description

Make filter fun. that returns the most abundant p fraction of taxa

Usage

topp(p, na.rm=TRUE)

Arguments

p	A numeric of length 1, indicating what fraction of the most abundant taxa should be kept.
na.rm	A logical. Should NAs be removed. Default is TRUE.

Value

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

See Also

topk, topf, topp, rm_outlierf

Examples

## Use simulated abundance matrix
set.seed(711)
testOTU <- otu_table(matrix(sample(1:50, 25, replace=TRUE), 5, 5), taxa_are_rows=FALSE)
sample_sums(testOTU)
f1  <- filterfun_sample(topp(0.2))
(wh1 <- genefilter_sample(testOTU, f1, A=1))
wh2 <- c(TRUE, TRUE, TRUE, FALSE, FALSE)
prune_taxa(wh1, testOTU)
prune_taxa(wh2, testOTU)

Example output

sa1 sa2 sa3 sa4 sa5 
 97 123 118 157 152 
  sp1   sp2   sp3   sp4   sp5 
FALSE FALSE  TRUE  TRUE FALSE 
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.