Description Usage Arguments Value Examples
This function summarizes taxa/pathway abundance tables to provide mean, sd, count by groups.
1 2 3 4 5 6 7 8 | taxa.meansdn(
taxtab,
sumvar,
groupvar,
percent.filter = 0.05,
relabund.filter = 5e-05,
othervar = "none"
)
|
taxtab |
taxa/pathway abundance table from phylum to species or any preferred highest taxa level. |
sumvar |
main variable for summary |
groupvar |
variable to be stratified. |
percent.filter |
prevalence threshold (the percentage of number of samples the taxa/pathway available). Default is 0.05. |
relabund.filter |
relative abundance threshold (the minimum of the average relative abundance for a taxa/pathway to be retained). Default is 0.00005. |
othervar |
vector of variables that are not abundance variables to be summarized. Default is "none". |
table of mean, sd, count by group.
1 2 3 | #Load summary tables of bacterial taxa relative abundance from Bangladesh data
data(taxtab6)
taxa.meansdn.rm<-taxa.meansdn(taxtab=taxtab6,sumvar="bf",groupvar="age.sample")
|
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