getCoreTaxa: List core taxa across groups

In hallucigenia-sparsa/seqgroup: Analysis of Sequencing Data with Groups

List core taxa across groups

Description

List the indices of all taxa that occur at least min.occ times in each group.

Usage

getCoreTaxa(
  x,
  groups = c(),
  min.occ = 1,
  min.groupnum = length(unique(groups)),
  consecutive = FALSE
)

Arguments

x	an abundance matrix where rows are taxa and columns samples
groups	group membership vector with as many entries as abundances has samples
min.occ	minimal occurrence to count a taxon as present in each group
min.groupnum	minimum occurrence across groups (fulfilling selected criteria within each group), by default in all
consecutive	assumes samples in each group are ordered by time, if true, minimal occurrence has to be consecutive

Value

indices of core taxa

Examples

data("floresgut_taxa")
data("floresgut_metadata")
groups=floresgut_metadata$host_subject_id
ct=getCoreTaxa(x=floresgut_taxa,groups=groups,consecutive=TRUE, min.occ=4)
rownames(floresgut_taxa)[ct]

hallucigenia-sparsa/seqgroup documentation built on July 6, 2022, 1:11 p.m.