twoGroupDEgenes: DE genes analysis for two groups.

In Tong-Chen/ImageGP: For ImageGP cloud platform (https://www.bic.ac.cn/BIC)

DE genes analysis for two groups.

Description

DE genes analysis for two groups.

Usage

twoGroupDEgenes(
  dds,
  groupA,
  groupB,
  design = "conditions",
  padj = 0.05,
  log2FC = 1,
  dropCol = c("lfcSE", "stat"),
  output_prefix = "ehbio",
  normalized_counts = NULL,
  lfcShrink = FALSE,
  ...
)

Arguments

dds	DESeq function returned object.
groupA	Group name 1.
groupB	Group name 2.
design	The group column name. Default "conditions".
padj	Multiple-test corrected p-value. Default 0.05.
log2FC	Log2 transformed fold change. Default 1.
dropCol	Columns to drop in final output. Default c("lfcSE", "stat"). Other options "ID", "baseMean", "log2FoldChange", "lfcSE", "stat", "pvalue", "padj". This has no specific usages except make the table clearer.
output_prefix	A string as prefix of output files.
normalized_counts	a data matrix of normalized counts or an object return by deseq2normalizedExpr. Default NULL.
...	Additional parameters given to ggsave.

Examples

twoGroupDEgenes(dds, "trt", "untrt")

Tong-Chen/ImageGP documentation built on April 14, 2025, 12:54 p.m.