phy_pruneTaxa: Remove taxa that have counts summing to n
In g-antonello/gautils2: Wrapper of my functions to wrangle mostly microbiome data
View source: R/phy_pruneTaxa.R
phy_pruneTaxa R Documentation
Remove taxa that have counts summing to n
Description
A simple wrapper function usable in a pipe that allows for quick pruning of a phyloseq object
Usage
phy_pruneTaxa(physeq, n = 0)
Arguments
physeq
A phyloseq object
n
A numeric number of the pruning threshold to filter out any taxon that sums to strictly less than that value
Value
A phyloseq object with only taxa with taxa_sums(physeq) > 0
Examples
data(enterotype)
entero_noPyro <- subset_samples(enterotype, SeqTech != "Pyro454")
# before pruning
entero_noPyro
# after pruning
prune0taxa(entero_noPyro)
g-antonello/gautils2 documentation built on Nov. 28, 2022, 9:39 a.m.
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View source: R/phy_pruneTaxa.R
| phy_pruneTaxa | R Documentation |
Remove taxa that have counts summing to n
Description
A simple wrapper function usable in a pipe that allows for quick pruning of a phyloseq object
Usage
phy_pruneTaxa(physeq, n = 0)
Arguments
physeq |
A |
n |
A |
Value
A phyloseq object with only taxa with taxa_sums(physeq) > 0
Examples
data(enterotype) entero_noPyro <- subset_samples(enterotype, SeqTech != "Pyro454") # before pruning entero_noPyro # after pruning prune0taxa(entero_noPyro)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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