taxcomtab.show {metamicrobiomeR}

Display abundance comparison results.

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)