run_LEfSe: Differential Expression Analysis by LEfSe Package

In HuaZou/MyRtools: Statistic Approaches on Data Analysis

Description

LEfSe method for microbiome biomarker discovery.

Usage

run_LEfSe(dataset=ExpressionSet,
                 trim="none",
                 transform="none",
                 normalize="none",
                 Group_info="Group",
                 Group_name=c("HC", "AA"),
                 kw.p=0.05,
                 wl.p=0.05,
                 Lda=2)

Arguments

trim,	Character; filter to apply.(default: trim="none").
transform,	Character; transformation to apply.(default: tranform="none").
normalize,	Character; normalization to apply.(default: normalize="none").
Group_info,	Character; design factor(default: "Group").
Group_name,	Character; (Required) the group for comparison.
kw.p,	Numeric; significant level of kruskal.test(default: 0.05).
wl.p,	Numeric; significant level of wilcox(default: 0.05).
Lda,	Numeric; LDA score(default: 2).
Expression,	ExpressionSet; (Required) ExpressionSet object.

Details

12/2/2021 Guangzhou China

Value

significant difference with enriched directors

Author(s)

Hua Zou

Examples

data(ExprSetRawCount)

LEfSe_res <- run_LEfSe(dataset=ExprSetRawCount, Group_info="Group", Group_name=c("HC", "AA"), kw.p=0.05, wl.p=0.05, Lda=2)
LEfSe_res

HuaZou/MyRtools documentation built on Jan. 6, 2022, 8:56 a.m.