taxcomtab.show: Display abundance comparison results.

In metamicrobiomeR: Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects

Description

This function displays taxa/pathway abundance comparison results as table.

Usage

taxcomtab.show(
  taxcomtab,
  sumvar = "taxa",
  tax.lev = "l2",
  tax.select = "none",
  showvar,
  readjust.p = FALSE,
  p.adjust.method = "fdr",
  p.cutoff = 0.05,
  digit = 2,
  p.digit = 4
)

Arguments

taxcomtab	table of taxa abundance comparison generated from taxa.compare.
sumvar	Options are "taxa" for bacterial taxa and "path" for pathway. Default is "taxa"
tax.lev	taxa level to be displayed. Options are from "l2" (phylum) to "l7" (species). Default is "l2".
tax.select	selected list of taxa to be displayed. Default is "none" or display all available taxa.
showvar	variable (pattern) in the model to be displayed.
readjust.p	multiple testing re-adjustment for only the level to be displayed (TRUE) or keep original multiple testing adjustment for all taxa of all levels (FALSE).
p.adjust.method	method for multiple testing adjustment. Available options are those of the p.adjust function. Default is "fdr".
p.cutoff	cutoff p-value to be displayed. Default is 0.05.
digit	digit for estimates and 95 CI. Default is 2.
p.digit	digit for p-values. Default is 4.

Value

a table of results.

Examples

#Load summary tables of bacterial taxa relative abundance from Bangladesh data
data(taxtab6)
tab6<-as.data.frame(taxtab6)
#Comparison of bacterial taxa relative abundance using GAMLSS
# Only run on a few taxa of a phylum to save running time
tl<-colnames(taxtab6)[grep("k__bacteria.p__fusobacteria",colnames(taxtab6))]
taxacom.ex<-taxa.compare(taxtab=tab6[,c("personid","x.sampleid","bf","age.sample",tl)],
propmed.rel="gamlss",comvar="bf",adjustvar="age.sample",
longitudinal="yes",p.adjust.method="fdr")
# show phylum results
taxcomtab.show(taxcomtab=taxacom.ex,tax.select="none",
showvar="bfNon_exclusiveBF", tax.lev="l2",
readjust.p=TRUE,p.adjust.method="fdr",p.cutoff = 1)

metamicrobiomeR documentation built on Nov. 9, 2020, 5:06 p.m.