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)
siamcat | an object of class siamcat |
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filter.method | method used for filtering the features, can be one of
these: |
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: |
verbose | control output: |
siamcat an object of class siamcat
This function