MPSE: Construct a MPSE object

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Construct a MPSE object

Description

Construct a MPSE object

Usage

MPSE(
  assays,
  colData = NULL,
  otutree = NULL,
  taxatree = NULL,
  refseq = NULL,
  ...
)

Arguments

assays	A 'list' or 'SimpleList' of matrix-like elements All elements of the list must have the same dimensions, we also recommend they have names, e.g. list(Abundance=xx1, RareAbundance=xx2).
colData	An optional DataFrame describing the samples.
otutree	A treedata object of tidytree package, the result parsed by the functions of treeio.
taxatree	A treedata object of tidytree package, the result parsed by the functions of treeio.
refseq	A XStingSet object of Biostrings package, the result parsed by the readDNAStringSet or readAAStringSet of Biostrings.
...	additional parameters, see also the usage of SummarizedExperiment.

Value

MPSE object

Examples

set.seed(123)
xx <- matrix(abs(round(rnorm(100, sd=4), 0)), 10)
xx <- data.frame(xx)
rownames(xx) <- paste0("row", seq_len(10))
mpse <- MPSE(assays=xx)
mpse

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.