Set to FALSE any outlier species greater than f fractional abundance.
This is for removing overly-abundant outlier taxa, not for trimming low-abundance taxa.
rm_outlierf(f, na.rm=TRUE)
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 |
A function (enclosure), suitable for filterfun_sample.
topk, topf,
topp, rm_outlierf
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.