sub_tax_summary {LorMe} | R Documentation |
Subsetting tax summary objects
Description
Subsetting tax summary objects
Usage
sub_tax_summary(taxobj, ..., specificnum = NULL, taxnum = NULL)
Arguments
taxobj |
tax summary objects computed by |
... |
logical expression that are are defined in terms of the variables in Groupfile of tax summary objects. See details in |
specificnum |
specific numbers indicating samples to keep based on Groupfile of tax summary objects. |
taxnum |
specific numbers indicating taxonomy to keep based on Base file |
Value
Subset of tax summary objects.Same as tax_summary
.
Author(s)
Wang Ningqi 2434066068@qq.com
Examples
data("Three_group")
# Check meta file
print(Three_group$Groupfile)
# Subsetting tax summary objects
# Select BF and OF groups
sub_testtax_summary <- sub_tax_summary(Three_group, Group %in% c("BF", "OF"))
print(sub_testtax_summary$Groupfile)
# Subsetting according to taxonomy
Proteo <- sub_tax_summary(
Three_group,
taxnum = which(Three_group$Base_taxonomy$Phylum == "p__Proteobacteria")
)
print(Proteo$Phylum_percent) # Check phylum table
print(Proteo$Genus_percent) # Check genus table
[Package LorMe version 1.2.1 Index]