biomarker: Identify biomarker by using randomForest method

Description Usage Arguments Value Author(s) Examples

Description

Identify biomarker by using randomForest method

Usage

1
2
3
4
5
6
7
8
biomarker(
  physeq,
  group,
  ntree = 500,
  pvalue = 0.05,
  normalize = TRUE,
  method = "relative"
)

Arguments

physeq

A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.

group

group. A character string specifying the name of a categorical variable containing grouping information.

ntree

Number of trees to grow. This should not be set to too small a number, to ensure that every input row gets predicted at least a few times.

pvalue

pvalue threshold for significant results from kruskal.test

normalize

to normalize the data before analysis(TRUE/FALSE)

method

A list of character strings specifying method to be used to normalize the phyloseq object Available methods are: "relative","TMM","vst","log2".

Value

data frame with significant biomarker

Author(s)

Kai Guo

Examples

1
2
data("Physeq")
res <- biomarker(physeq,group="group")

microbial documentation built on April 2, 2021, 1:06 a.m.