biomarker: Identify biomarker by using randomForest method

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Identify biomarker by using randomForest method

Description

Identify biomarker by using randomForest method

Usage

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

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

microbial documentation built on May 29, 2024, 5:51 a.m.