This function may convert absolute abundances into relative abundances and then performs unsupervised feature filtering. Features can be filtered based on abundance or prevalence. Additionally, unmapped reads may be removed.

filter.feat(siamcat, filter.method = "abundance", cutoff = 0.001,
  recomp.prop = FALSE, rm.unmapped = TRUE, verbose = 1)

Arguments

siamcat

an object of class siamcat

filter.method

method used for filtering the features, can be one of these: c("abundance", "cum.abundance", "prevalence")

cutoff

float, abundace or prevalence cutoff

recomp.prop

boolean, should absolute abundances be converted into relative abundances?

rm.unmapped

boolean, should unmapped reads be discarded?

verbose

control output: 0 for no output at all, 1 for standard information, defaults to 1

verbose

control output: 0 for no output at all, 1 for only information about progress and success, 2 for normal level of information and 3 for full debug information, defaults to 1

Value

siamcat an object of class siamcat

Details

This function