Make filter fun. that returns the top f fraction of taxa in a sample.
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.
topf(f, na.rm=TRUE)
f |
Single numeric value between 0 and 1. |
na.rm |
Logical. Should we remove NA values. Default |
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.
topk, topf,
topp, rm_outlierf
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.