run_edgeR: Differential Expression Analysis by edgeR Package
In HuaZou/MyRtools: Statistic Approaches on Data Analysis

Description Usage Arguments Details Value Author(s) Examples

edgeR requires the count data (a matrix of integer values) to input.

run_edgeR(dataset=ExpressionSet,
                 trim="none",
                 Group_info="Group",
                 Group_name=c("HC", "AA"),
                 Pvalue=0.05,
                 Log2FC=1)

`trim,`	Character; filter to apply.(default: trim="none").
`Group_info,`	Character; design factor(default: "Group").
`Group_name,`	Character; (Required) the group for comparison.
`Pvalue,`	Numeric; significant level(default: 0.05).
`Log2FC,`	Numeric; log2FoldChange(default: 1).
`Expression,`	ExpressionSet; (Required) ExpressionSet object.

12/2/2021 Guangzhou China

a list object: edgeR results significant difference with enriched directors

Hua Zou

data(ExprSetRawCount)

edgeR_res <- run_edgeR(dataset=ExprSetRawCount, Group_info="Group", Group_name=c("HC", "AA"), Pvalue=0.05, Log2FC=1)
edgeR_res$res